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No, it should not f**k it up. tvseries will remember which eps you watched, for moving pictures, i cant say for sure. If you're using trakt or follw.it there should not be any problem with that either.

It will take a while for it to sync to the new paths though, but thats the only thing.

I have changed the paths for both tvseries and moving pictures a couple of times, and it never f**ked up my databases.