I'm currently going with my installation, I'm using the install tool that I found with some google (Dunno if it changes anything). Sadly i Didnt made a copy before trying a clean reinstall, but considering I'm doing an installation right now with the exact same mods this are the mods that were installed before: (Same ones as before)
I tried to reproduce it again, but no luck. I'm thinking maybe some kind of problem i might have had on the early installation (I had some problems where i had to manually download and extract some mods, and it was a bit messy, this time around I was more careful). The problem at that time happened both when installing through the tool and when using the weidu setup
On the support forum for the Tool another user seemed to have had the same problem when trying a second install over an existing installation, and went away once he started from scratch, in my case I had a problem (I think a missing essential mod) that stopped my installation, and i tried to start again after fixing it. Anyways, it doesn't seem to be a common problem, and it seems to be linked to some weird interaction when the install tool is stopped for some reason (or so i think, based on the reports so far), and easy enough to fix, so no need to worry yourself over it
Thanks for the help, appreciate it