[HELP] Huge issue with AC installation and content manager

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I got an ssd for my pc the other day, Installed windows and all that stuff. I installed content manager and pointed it to my AC (now on a second hard drive which used to be my boot drive). It then went on to screw up my AC install, deleting my JSGME mods folder, weather folder (?) and worst, my tracks folder (with about 200 or so tracks). I don't know what to do, if anyone has any ideas that would be really appreciated. I have never had CM do anything like this before in my 3 years of using it