When loading a saved project the wav files associated with it don't load due to misplaced files. When I tracked the files locations they are in the correct place but wrong folder(?). Should I uninstall and reinstall?
. . . . in the correct place but wrong folder(?) . . . .
A bit of a long shot, are you using OneDrive and they ending up in the 'OneDrive/Documents' folder?
If so, at a minimum you need to stop OneDrive putting, syncing, the files in the Cloud, see this article on how to do this, which folder(s) to stop syncing depends on how you have organised your storage.
If not using OneDrive, then can you clarify what correct place/wrong folders are, ie the folder locations of where they are and Music Maker thinks they should be.
A screen shot of the Music Maker Settings, shortcut P key, Folders tab would help.