FILE menu|SAVE PROJECT FILE AS (or SAVE AS) creates a VPJ fiile that maps the path for the files, and the layout of all clips, transitions, effects, etc.
If a file is moved or its name or extension changed, VP can't find it and will prompt to resolve. If you locate the file, VP will remap its VPJ file to the new location. Once this is done, resave the project.
Bottom line: do not move or rename files that VP needs to reconstruct a project. Use FILE|SAVE PROJECT FILE AS routinely, with an incremental number, to ensure that all elements are up-to-date when the project is reloaded, and older incarnations are retained. If FILE|SAVE is instead used, the existing VPJ file will be overwritten.