Just so you guys know, here is something I found out the first week of 5.2:
Prior to 5.2 I was playing combat with assassination off spec.
My weapons were double upgraded normal gara'kal for mh, and double upgraded LFR spiritsever for OH
For assassination my weapons were double upgraded spiritsever for mh (my combat offhand), and nonupgraded lfr stone guard for offhand.
First week of 5.2, I get normal spiritsever with a coin roll. The problem here is that the 496 spiritsever is an ideal offhand for combat, but I already had a crystallized dread in the double upgraded LFR spiritsever, so I couldn't put the sha gem in the normal spiritsever.
Just to get rid of the sha gem from the LFR dagger, I dropped the dagger off in void storage to clear the gem and enchant, so that I could get a new sha gem for the normal mode spiritsever.
As it so turns out, dropping the dagger in void storage DID NOT clear the double-upgraded status. The LFR dagger remained at 491. (I did have to re-enchant it with dancing steel, though).
So, for whatever reason, if you need to clear a sha gem and the weapon is upgraded, void storage will not reduce the item level of that weapon (be warned, that blizz may stealth nerf that).