I don't see how you get this.
But some pointers:
Make sure all VIs are under one folder.
Make sure all other versions of the files are not searchable (remove a backup-folder from your LabVIEW search paths)
Create a LVproject.
Add the main VI to the project.
Open the main VI from the project
If you get warnings, go over them one by one and select the VI you want to keep.
Switch over to files view (available in 8.5 ctrl-e) and see if the VIs are in the expected locations, if not, open them (from the project), File-> save as (update callers)
This will get your project cleaned up.
From now on you only use the project window.
To make a backup-file, create a source-distribution, where you will rename each file (a feature available in 8.5)
If you don't rename the files make sure you always close the project and any of it's files before opening a VI from the backup folder.
Ton