I accidentally broke 2 of my compacting drawers and when I replaced them I noticed the status upgrades (III) were missing. There weren't returned when the drawer was broken. This may not be a bug, this may be intentional, but as the level upgrades are returned shouldn't the status upgrade? (I didn't actually get a level upgrade since I didn't put on in this case).

Sounds like a bug, the intention is to get them back. When the 1.2 update comes, there will be an upgrade inventory, so there would be even more expectation for them to drop.