Welcome to the world of pain that is the misbehaving project!
You may have some success by manually editing the .lvproj file (it is just a text file) and removing the dependencies there (the ones which have the bad linking), then adding them back in if you can get your project stable.
Please make a backup of the .lvproj file and in fact everything!
Even with 8.5 the project file still seems quite fragile. Kid gloves are, in my experience, very necessary.
Good luck with resolving your issues.