Here, when a folder containing used and unused project files plus the VPJ control file is moved, VP has no trouble finding the files. Moving the VP project folder into your raw footage folder, as a subfolder, should not disturb the paths.
In several tests, even when the VP folder was moved as a subfolder to a different drive, invoking the VPJ in that folder found all the files.
Before making a move, SAVE PROJECT FILE AS, giving it a unique # or name, so as to not overwrite earlier saves. Then the pointers should be up to date.
https://www.nch.com.au/suggestions/index.html?software=VideoPad&version=8.77