The details are a little sketchy, but I'll put out a couple things that might be going on...
I'm assuming that you can find the VI manually. Therefore what you need to do is open everything and find the "missing" VI. Once everything is open, do a Save All.
One possible issue is that to speed loading, LV stores the link to a subVI and the last known path to it. Problem arise however, if during a load it can't find a subVI in the last known place. LV immediately starts doing a search. Eventually, if it can't find it, LV puts up a dialog box asking you to find it manually.
Once you find the VI, LV relinks to the VI in the new location. However, this new path doesn't get changed unless you do a save.
Mike...