Had over 300 stacks of cobble in a vast storage unit. After leaving the area and returning the next time I started the game the Vast Storage unit was empty. simplelabels-1.8.9-0.0.4

Odd. Did your game crash between loads or did you exit normally?

I exited normally. No error signs.

1. put over 300 stacks of cobble in the vast storage unit
2. leave area and do some exploring
3. end game and do something else
4. restart minecraft and return to location of Vast Storage Unit
5. label was black and all cobble was gone
6. breaking and placing it back made no difference

I am unable to reproduce this in testing. For some more information, was this single player or on a server? Was your area chunkloaded?

Single player
no chunckloading implemented

Maybe something happened during exploring, though it's doubtful.