Do you mean try to put the original secure.htaccess back first? That's what kept disappearing and I had to edit it to make it stop doing that.
The downloaded root .htaccess was missing most of the code I thought I'd managed to put back in. I replaced it first with the version on my computer that I had thought was working:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
# BULLETPROOF .47.5 >>>>>>> SECURE .HTACCESS
# If you edit the BULLETPROOF .47.5 >>>>>>> SECURE .HTACCESS text above
# you will see error messages on the BPS Security Status page
# BPS is reading the version number in the htaccess file to validate checks
# If you would like to change what is displayed above you
# will need to edit the BPS /includes/functions.php file to match your changes
# If you update your WordPress Permalinks the code between BEGIN WordPress and
# END WordPress is replaced by WP htaccess code.
# This removes all of the BPS security code and replaces it with just the default WP htaccess code
# To restore this file use BPS Restore or activate BulletProof Mode for your Root folder again.
# BEGIN WordPress
# IMPORTANT!!! DO NOT DELETE!!! - BEGIN WordPress above or END WordPress - text in this file
# They are reference points for WP, BPS and other plugins to write to this htaccess file.
# IMPORTANT!!! DO NOT DELETE!!! - BPSQSE BPS QUERY STRING EXPLOITS - text
# BPS needs to find the - BPSQSE - text string in this file to validate that your security filters exist
# TURN OFF YOUR SERVER SIGNATURE
ServerSignature Off
# ADD A PHP HANDLER
# If you are using a PHP Handler add your web hosts PHP Handler below
# DO NOT SHOW DIRECTORY LISTING
# If you are getting 500 Errors when activating BPS then comment out Options -Indexes
# by adding a # sign in front of it. If there is a typo anywhere in this file you will also see 500 errors.
Options -Indexes
# DIRECTORY INDEX FORCE INDEX.PHP
# Use index.php as default directory index file
# index.html will be ignored will not load.
DirectoryIndex index.php index.html /index.php
# BPS PRO ERROR LOGGING AND TRACKING - Available in BPS Pro only
# BPS Pro has premade 403 Forbidden, 400 Bad Request and 404 Not Found files that are used
# to track and log 403, 400 and 404 errors that occur on your website. When a hacker attempts to
# hack your website the hackers IP address, Host name, Request Method, Referering link, the file name or
# requested resource, the user agent of the hacker and the query string used in the hack attempt are logged.
# BPS Pro Log files are added to the P-Security All Purpose File Manager to view them.
# All BPS Pro log files are htaccess protected so that only you can view them.
# The 400.php, 403.php and 404.php files are located in /wp-content/plugins/bulletproof-security/
# The 400 and 403 Error logging files are already set up and will automatically start logging errors
# after you install BPS Pro and have activated BulletProof Mode for your Root folder.
# If you would like to log 404 errors you will need to copy the logging code in the BPS Pro 404.php file
# to your Theme's 404.php template file. Simple instructions are included in the BPS Pro 404.php file.
# You can open the BPS Pro 404.php file using the WP Plugins Editor or by using the BPS Pro File Manager.
# NOTE: By default WordPress automatically looks in your Theme's folder for a 404.php template file.
# ErrorDocument 400 /wp-content/plugins/bulletproof-security/400.php
# ErrorDocument 403 /wp-content/plugins/bulletproof-security/403.php
ErrorDocument 404 /404.php
# DENY ACCESS TO PROTECTED SERVER FILES - .htaccess, .htpasswd and all file names starting with dot
RedirectMatch 403 /\..*$
RewriteEngine On
RewriteBase /
RewriteRule ^wp-admin/includes/ - [F,L]
RewriteRule !^wp-includes/ - [S=3]
RewriteRule ^wp-includes/[^/]+\.php$ - [F,L]
RewriteRule ^wp-includes/js/tinymce/langs/.+\.php - [F,L]
RewriteRule ^wp-includes/theme-compat/ - [F,L]
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
# PLUGINS AND VARIOUS EXPLOIT FILTER SKIP RULES
# IMPORTANT!!! If you add or remove a skip rule you must change S= to the new skip number
# Example: If RewriteRule S=5 is deleted than change S=6 to S=5, S=7 to S=6, etc.
# Adminer MySQL management tool data populate
RewriteCond %{REQUEST_URI} ^/wp-content/plugins/adminer/ [NC]
RewriteRule . - [S=12]
# Comment Spam Pack MU Plugin - CAPTCHA images not displaying
RewriteCond %{REQUEST_URI} ^/wp-content/mu-plugins/custom-anti-spam/ [NC]
RewriteRule . - [S=11]
# Peters Custom Anti-Spam display CAPTCHA Image
RewriteCond %{REQUEST_URI} ^/wp-content/plugins/peters-custom-anti-spam-image/ [NC]
RewriteRule . - [S=10]
# Status Updater plugin fb connect
RewriteCond %{REQUEST_URI} ^/wp-content/plugins/fb-status-updater/ [NC]
RewriteRule . - [S=9]
# Stream Video Player - Adding FLV Videos Blocked
RewriteCond %{REQUEST_URI} ^/wp-content/plugins/stream-video-player/ [NC]
RewriteRule . - [S=8]
# XCloner 404 or 403 error when updating settings
RewriteCond %{REQUEST_URI} ^/wp-content/plugins/xcloner-backup-and-restore/ [NC]
RewriteRule . - [S=7]
# BuddyPress Logout Redirect
RewriteCond %{QUERY_STRING} action=logout&redirect_to=http%3A%2F%2F(.*) [NC]
RewriteRule . - [S=6]
# redirect_to=
RewriteCond %{QUERY_STRING} redirect_to=(.*) [NC]
RewriteRule . - [S=5]
# Login Plugins Password Reset And Redirect 1
RewriteCond %{QUERY_STRING} action=resetpass&key=(.*) [NC]
RewriteRule . - [S=4]
# Login Plugins Password Reset And Redirect 2
RewriteCond %{QUERY_STRING} action=rp&key=(.*) [NC]
RewriteRule . - [S=3]
# TIMTHUMB FORBID RFI and MISC FILE SKIP/BYPASS RULE
# Only Allow Internal File Requests From Your Website
# To Allow Additional Websites Access to a File Use [OR] as shown below.
# RewriteCond %{HTTP_REFERER} ^.*YourWebsite.com.* [OR]
# RewriteCond %{HTTP_REFERER} ^.*AnotherWebsite.com.*
RewriteCond %{QUERY_STRING} ^.*(http|https|ftp)(%3A|:)(%2F|/)(%2F|/)(w){0,3}.?(blogger|picasa|blogspot|tsunami|petapolitik|photobucket|imgur|imageshack|wordpress\.com|img\.youtube|tinypic\.com|upload\.wikimedia|kkc|start-thegame).*$ [NC,OR]
RewriteCond %{THE_REQUEST} ^.*(http|https|ftp)(%3A|:)(%2F|/)(%2F|/)(w){0,3}.?(blogger|picasa|blogspot|tsunami|petapolitik|photobucket|imgur|imageshack|wordpress\.com|img\.youtube|tinypic\.com|upload\.wikimedia|kkc|start-thegame).*$ [NC]
RewriteRule .* index.php [F,L]
RewriteCond %{REQUEST_URI} (timthumb\.php|phpthumb\.php|thumb\.php|thumbs\.php) [NC]
#RewriteCond %{HTTP_REFERER} ^.*demo5.local.*
RewriteRule . - [S=1]
# BPSQSE BPS QUERY STRING EXPLOITS
# The libwww-perl User Agent is forbidden - Many bad bots use libwww-perl modules, but some good bots use it too.
# Good sites such as W3C use it for their W3C-LinkChecker.
# Add or remove user agents temporarily or permanently from the first User Agent filter below.
# If you want a list of bad bots / User Agents to block then scroll to the end of this file.
RewriteCond %{HTTP_USER_AGENT} (havij|libwww-perl|wget|python|nikto|curl|scan|java|winhttp|clshttp|loader) [NC,OR]
RewriteCond %{HTTP_USER_AGENT} (%0A|%0D|%27|%3C|%3E|%00) [NC,OR]
RewriteCond %{HTTP_USER_AGENT} (;|<|>|'|"|\)|\(|%0A|%0D|%22|%27|%28|%3C|%3E|%00).*(libwww-perl|wget|python|nikto|curl|scan|java|winhttp|HTTrack|clshttp|archiver|loader|email|harvest|extract|grab|miner) [NC,OR]
RewriteCond %{THE_REQUEST} \?\ HTTP/ [NC,OR]
RewriteCond %{THE_REQUEST} \/\*\ HTTP/ [NC,OR]
RewriteCond %{THE_REQUEST} etc/passwd [NC,OR]
RewriteCond %{THE_REQUEST} cgi-bin [NC,OR]
RewriteCond %{THE_REQUEST} (%0A|%0D|\\r|\\n) [NC,OR]
RewriteCond %{REQUEST_URI} owssvr\.dll [NC,OR]
RewriteCond %{HTTP_REFERER} (%0A|%0D|%27|%3C|%3E|%00) [NC,OR]
RewriteCond %{HTTP_REFERER} \.opendirviewer\. [NC,OR]
RewriteCond %{HTTP_REFERER} users\.skynet\.be.* [NC,OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=http:// [OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=(\.\.//?)+ [OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=/([a-z0-9_.]//?)+ [NC,OR]
RewriteCond %{QUERY_STRING} \=PHP[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12} [NC,OR]
RewriteCond %{QUERY_STRING} (\.\./|\.\.) [OR]
RewriteCond %{QUERY_STRING} ftp\: [NC,OR]
RewriteCond %{QUERY_STRING} http\: [NC,OR]
RewriteCond %{QUERY_STRING} https\: [NC,OR]
RewriteCond %{QUERY_STRING} \=\|w\| [NC,OR]
RewriteCond %{QUERY_STRING} ^(.*)/self/(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} ^(.*)cPath=http://(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*embed.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^e]*e)+mbed.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*object.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^o]*o)+bject.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*iframe.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^i]*i)+frame.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [NC,OR]
RewriteCond %{QUERY_STRING} base64_(en|de)code[^(]*\([^)]*\) [NC,OR]
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} ^.*(\[|\]|\(|\)|<|>|%3c|%3e|%5b|%5d).* [NC,OR]
RewriteCond %{QUERY_STRING} ^.*(\x00|\x04|\x08|\x0d|\x1b|\x20|\x3c|\x3e|\x5b|\x5d|\x7f).* [NC,OR]
RewriteCond %{QUERY_STRING} (NULL|OUTFILE|LOAD_FILE) [OR]
RewriteCond %{QUERY_STRING} (\./|\../|\.../)+(motd|etc|bin) [NC,OR]
RewriteCond %{QUERY_STRING} (localhost|loopback|127\.0\.0\.1) [NC,OR]
RewriteCond %{QUERY_STRING} (<|>|'|%0A|%0D|%27|%3C|%3E|%00) [NC,OR]
RewriteCond %{QUERY_STRING} concat[^\(]*\( [NC,OR]
RewriteCond %{QUERY_STRING} union([^s]*s)+elect [NC,OR]
RewriteCond %{QUERY_STRING} union([^a]*a)+ll([^s]*s)+elect [NC,OR]
RewriteCond %{QUERY_STRING} \-[sdcr].*(allow_url_include|allow_url_fopen|safe_mode|disable_functions|auto_prepend_file) [NC,OR]
RewriteCond %{QUERY_STRING} (;|<|>|'|"|\)|%0A|%0D|%22|%27|%3C|%3E|%00).*(/\*|union|select|insert|drop|delete|update|cast|create|char|convert|alter|declare|order|script|set|md5|benchmark|encode) [NC,OR]
RewriteCond %{QUERY_STRING} (sp_executesql) [NC]
RewriteRule ^(.*)$ - [F,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
# DENY BROWSER ACCESS TO THESE FILES
# wp-config.php, bb-config.php, php.ini, php5.ini, readme.html
# Replace Allow from 88.77.66.55 with your current IP address and remove the
# pound sign # from in front of the Allow from line of code below to access these
# files directly from your browser.
<FilesMatch "^(wp-config\.php|php\.ini|php5\.ini|readme\.html|bb-config\.php)">
Order allow,deny
Deny from all
#Allow from 88.77.66.55
</FilesMatch>
# IMPORTANT!!! DO NOT DELETE!!! the END WordPress text below
# END WordPress
The secure.htaccess was also incomplete, so I replaced that first too.
Then I followed your instructions. At step 4, the secure.htaccess was back to the original version rather than what I thought I had just uploaded -- it had the FORBID EMPTY REFFERER SPAMBOTS and REQUEST METHODS FILTERED code back in it. However, I followed your directions exactly, and copy-pasted it into the downloaded root .htaccess and re-uploaded that, overwriting the one that was on the server. I changed the permissions to 644. The file immediately disappeared and the 404 errors were back.
I've re-uploaded the file that has the above code, both in the root as .htaccess with 604 permissions, and in the BPS admin/htaccess folder as secure.htaccess with 644 permissions, and all is working again.
[Moderator Note: Please use the pastebin for large blocks of code. 250 lines of .htaccess directives is just a little excessive.]