Hello all,
Most likely, the problem is that the subVIs were saved with a different name, or changes were made to it that didn't allow it to be placed correctly back into the mainVI (different input/output terminals, etc). I would just get your mainVI open, and look around for the missing subVIs (the ones with large questions marks). You can then determine what was supposed to be placed there and right-click on the question mark box and choose "Replace" and then use the "Select a VI..." option to replace the unknown box with the correct VI. Also, BJD1613's recommendation about saving VIs is a good one for future reference.
I hope this helps! Have a great day!
Liz Fausak