so I have two unite folders "unite" and "unite2" sitting parallel to the public_html folder. Unite restores the site in public_html/main and unite2 restores the site in public_html/main/ssc.
When I first started using Unite it seemed to work fine, but sometimes, the restoration does not complete. When I visit the site, i get a 500 error. When I ftp to the files, the installation folder is still there, and or the .htaccess file with the Joomla specific, bot blocking, or other directives is deleted and replaced with a basic .htaccess file. Sometimes, the installation folder has been removed, but again the .htaccess file has been deleted or overwritten. I tried packing the .htaccess file from my primary site into the archive, but that did not have any effect.
I have checked with my host to verify that my cron job is set to use the Php Cli binary and my hosting account has Php 5.5.3. What else could be causing incomplete restorations?