Mod organizer deleted files. Now won`t sync with loot

[Strawb]

I have already installed Mod organizer 2.7. I tried to up grade to Mod organizer 2.8. Started the install and the install asked if I wanted to keep my mods, down loads and profiles.  So I clicked yes and it then began to delete every thing starting with my down loads. I luckily had task manager running so was able to terminate the program. But it had in only about thirty seconds deleted about forty gigs of zipped mods. So I manually deleted all traces of the mod organizer install including app data files. I then reinstalled mod organizer 2.7 with out any trouble. But now loot will not sync with mod organizer. It was working Ok before.