With your explanation, I think I can reconstruct what went wrong. I recently downloaded a new "stuff" build of XMPlay, and I accidentally launched it from Windows' Downloads folder. In that case, no plugins were obviously present and all priority file types were lost, and the settings were lost even after copying xmplay.exe to its intended destination.
It seems like not deleting the priority filetypes would be a safer choice. Sure, it means that some data could clutter up xmplay.ini, but then again it's not a lot of data, and it would only be potentially noticeable if you regularly add and remove new plugins while also editing their priority filetypes.