I'm really not sure of the best way to check this, but as you may know, your LabVIEW Projects (.lvproj files) are actually XML files containing all sorts of meta-data. this includes dependency paths, etc. so it may be part of your problem. I THINK they regenerate if they get erased or corrupted, but I would still back anything up before you touch them.
I would try a file compare tool like you can find online. I use a plugin for the free Notepad++.
Since you are using VeriStand, this could be even more complicated. I am not familiar with that product.
It might be a good idea to post both of your projects here too. There are gurus here that really understand everything going on behind the scenes of LabVIEW Projects. Failing that, you may need to contact NI customer support.
LabVIEW Pro Dev & Measurement Studio Pro (VS Pro) 2019