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When you disable all the options in .htaccess Maker the generated .htaccess is the same as the htaccess.txt that ships with Joomla! (with all of its optional, commented-out and therefore inactive stuff not present). This means that what you describe can't happen. Restoring your .htaccess, presumably to one based on the stock Joomla! .htaccess, would be equivalent to disabling all .htaccess Maker features. I can only think of two cases:

• You forgot to use the "Save and create .htaccess" button in the .htaccess Maker after disabling all settings
• Your original .htaccess contains custom directives, e.g. directives used to enable a specific version of PHP on your host. Such directives can be added to the .htaccess file generated by the .htaccess Maker using the "Custom .htaccess rules" section of its configuration page. Such rules can't, of course, be added automatically and their absence can cause an old version of PHP to be activated, leading to blank pages on your site.