404 redirects and rewritten htacess after disabled plugin

I keep getting errors on my site after I’ve disabled the ithemes plugin, removed database tables and rewrote all my htaccess files. Here’s what’s happening.

I have two subdirectories. directory a and directory b

my htaccess file from directory b starts off at:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /directoryb/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /directoryb/index.php [L]
</IfModule>

# END WordPress

I get everything working, both sites work fine. Then I come back a day later and all my pages (except homepage) on the directory b site redirect to a 404 on the directory a site. and my htaccess file on the directory b site looks like:

# 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

The url’s are correct for the pages, but they are not loading the correct content. Any ideas why this keeps happening? I didn’t have this problem before using this plugin, so I can only guess some setting caused this and even though I can temporarily fix the issue, it keeps reverting back to this error.

https://wordpress.org/plugins/better-wp-security/