I don't know how to prevent this, maybe you should call NI. But I have some suggestions. When backing up files, copy them into a directory called backup or something unique. Leave the originals where they are. When opening Labview, if it finds the backup files instead of the originals, don't save the vi. You can check to see if the sub-vi's that were loaded are the ones you desire by looking at the VI Hierarchy with full path name display turned on. I've run into the same problem many times. If I see that a sub-vi is coming from the wrong directory, I will replace the vi manually with the right one, check the hierarchy again to make sure, then save the vi. Next time I open it, everything is coming from where it should. I know this doesn't answer your orig
inal question, and could be a pain to replace many sub-vi's, but it works.