No problem here, just a curiosity:
After I had changed some indexing settings for a certain Category of Posts, I immediately got an alert from BPS and had to reactivate it (for the .htaccess files).
Should that have happened and/or have been necessary?
http://wordpress.org/extend/plugins/bulletproof-security/
It just happened again, and I had not been doing any clicking anywhere.
If you change your permalinks then this will automatically overwrite your root .htaccess file. After you have finished making changes to your permalink structure then you would create new .htaccess files.
if you are using another plugin that is incorrectly/inappropriately using the WordPress flush_rewrite_rules function then these plugins will wipe out/overwrite your root .htaccess file. I know of at least 20 plugins that are incorrectly/inappropriately using the WordPress flush_rewrite_rules function
http://forum.ait-pro.com/forums/topic/read-me-first-free/#flush-rewrite-rules
Cool beans, all set again...and many thanks for the insight.