I can't give this warning without minor spoilers. So be warned.
 
When you enter Silverlite Mine all your gear is taken away from you as a plot mechanic. You get your gear back by escaping prison and fighting 3 enemies to get 3 sets of gear back. The last set of gear (main player char) and the misc inventory items are supposed to reside in a chest right outside of the room where the final boss is.
 
If you imported your character from Origins there is a large possibility that the chest will be empty and you loose the 4th set and misc inventory items. Apparently it happens because of some DLC items from the Origins campaign.  Which ones is still unknown. But for the reference I had Wade's superior Medium armor and Helm Of Honoleth, not sure about the weapons and jewelry, but they get lost too.
 
So be sure to save your game just before you transition to SIlverlite Mine! The game will not do it for you!
 
My only solution was to take clothes off of every char and put it in the storage chest, along with all the items and go completely bare-assed to the Silverlite Mine. The fight is much more harder with the few items that you collect before the boss fight (even on easy) but at least you don't loose any items.

My main character gear was on an experimental subject just like my other characters' gear. I don't have any of the DLC though.

Man, there seems to be a *lot* of bugs regarding character equipment, especially relating to DLC gained stuff. I really wish DLC had the quality control that a full retail product had. Make no mistake: Awakening is on the DLC spectrum of this, not expansion pack. Then again, looking back on the Baldur's Gate 2 expansion pack, there were also a ton of new bugs introduced :\
 
Oh, by the way, I didn't have this problem. Besides a bunch of my DLC equipment (mostly related to the the Warden's Keep DLC) just missing upon import, I was still able to recover all my other stuff from the chest at the end of the mine.

??? 
I found my stuff on an experimental subject, just like the others.  All my additional stuff like potions, gifts etc. was in the chest, yeah, but not my character's personal equipment.

Equipped items are found on the experimental test subjects. Your regular inventory is found in the chest.

Went through the mine totally fine, 3rd fight with the experimental subjects had 2 of them, one with Ander's gear and one with my gear. The rest of my stuff was located in a chest next to the Quanari merchant.

Yeah the whole import thing is a lil buggy in Awakening.  I did that part your talking about with no problem, but when I first imported my character I had some stuff missing.  However it did clone Duncans Dagger and Sword you get in the Return to Ostagar DLC.  It was weird, it made a clone of them in Dragon bone (Which i think is what they always were) and one of them in red steel.

Not to dredge up this old chestnut but it seems like the bug causes the fourth experimental subject to not spawn at all. It just happened to me and since my last save was from 5 hours ago I think I'm just going to give up on beating Awakening and move on to Dragon Age 2. It's a real shame Bioware fucked it up this badly. Not game-breaking but certainly spirit-breaking.