SixStarJolteon You can safely copy your saves and Tray files to the new folder. While it's possible some of your old saves are broken, they can't break any content in the new folder. (That is not necessarily true for mod-related data that sits inside the save folder, so don't bring that over if you have any.) Mods and custom content are a different story; if you have any, test those files first before moving over your saves.
It would also not be a big deal to break the new folder, since it presumably doesn't have much, if any, content you'd want to save. You could simply delete it and resume testing in another new folder.
Since this thread is somewhat old, I'll lock it here. But feel free to start a new one if you still need help.