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I just transferred my live website to a test domain for development. There were no problems with previous transfers, but now that I have enabled SEO rewrites and am using an SSL cert something has gone wrong and VQMod does not seem to be working correctly. I deleted the vqmod cache files and mods.cache and they have not regenerated.

This thread has some similar issues, but it didn't seem to be resovled ..
http://forum.opencart.com/viewtopic.php?f=131&t=68357

Wow ... after about 40hrs of work it is resolved! I used one of the tips in the thread above ...

1. backup xml folder into a zip
2. delete vqmod folder
3. upload vqmod from a fresh download from the vqmod page
4. unzip vqmod and drop into root folder
5. delete xml folder and replace with the backup created in Step 1