I was curious to see if there were any dependency errors listed, however, I can see from your screenshots there are not. It still sounds to me like some dependency issue lies with the project and the method used to remove VIs from the project. I am curious, if you were to open each VI used in this project and save a duplicate (not by copy/paste but actually File>>Save As>>Copy>>Substitute copy for original) to your desktop. Then in a new project file add these files to the project. Does this issue still occur?
This should retain the integrity of your original project file if you do not modify the file location of the VIs referenced by your original project. What I am recommending is to save copies of your VIs using LabVIEW to a folder and adding them to a fresh project.
-Bob