Nope, all soul gems are lumped together, filled and unfilled.

Maybe I'm just lucky.

Make a save and try the suggestion that I posted above...

Yeah, stacks seem the least likely to blank in my experience too. But in my testing, it only seemed foolproof (given my limited data) if moving the entire stack in either direction -- and since it *has* to be a stack, any less than six is a pure crapshoot. Even with the stacks though, as I mentioned awhile ago, they can still get "maked" but appear intact until moving them to an otherwise reliable inventory -- i.e. a followers.**

I know this isn't a game-breaking bug but, nonetheless, it's definitely the most annoying one I've bumped into since all the seeming workarounds are also either bugged or limit RP options.

** Edit: I should clarify this I think with one of my tests in Breezehome:

Have ten filled lesser soul gems in my inventory (no blanks) and transfer the whole stack to an otherwise empty container; they stay intact. I move the whole stack back to my inventory; they stay intact. I move partial stack (seven of the ten) to my follower's inventory (again no blanks); the stack of seven loses their souls.

When moving entire stacks, one thing that I found that works with grand, greater, and sometimes common, is to place all you empty gems in a separate container, before trying to retrieve any filled gems. In other words, make sure that you only have filled gem in you inventory, then remove the filled gems that you want from the container. Once that is done, you can then retrieve any empty gems that you want.

Hmmm, I'll have to experiment with that a little more tomorrow. As I said, in my tests I was working with no blanks being present in any inventory/container throughout the process. However, I didn't test the behavior if there were already filled gems of the same type (and value) already present in the inventory/container. Again, I'll check that tomorrow ...

Soul gems will lose charges if dropped. Soul gems smaller than Grand have a very small chance of losing charges if placed in containers. The rate is like 5%. This bug is still in effect as of today.

The low rate and more importantly, the fact this bug does not affect Grand Soul Gems should alleviate your fears somewhat.

Yeah, I did notice that the grands seemed to remain intact. However, the 5% rate for the others (especially common and lower) is widely off the mark in my experiments. In fact, in my tests, it was either 0% or 100%, the only determining factor being whether full or partial stacks were moved (individuals seemed more random, though, and might fall into a rough % range if enough tests were run).

My soul gems almost never stacks so I'm moving them into a container one by one. At the end of moving roughly 20 filled gems of various sizes, one or two will appear in the container as unfilled.

Just dont store soul gems then. Just keep track of what vendors sell filled soul gems and focus your time on getting gold instead. Just buy filled soul gems whenever you need them.

Aahh ... mine mostly stack** so I'll have to see what happens (tomorrow) when I move the stack one at a time, though I'm not sure this will be the same as moving "true" individuals since stacks seem to have a mind of their own, so to speak.

** One thing I've found is that if my soul gems aren't stacking properly in my inventory, going to the weapons charge menu will fix this, at least temporarily -- eventually they'll start misbehaving again if I haven't had to recharge anything in awhile.

Yeah, one of the things I'm struggling with is my hoarding behavior when it comes to soul gems (stems from Oblivion when I used to place them around darker areas in friendly abodes to add ambience). I don't have much of a problem filling common and lower gems given my current lvl and RP where my bow has fiery soul trap.

Most of the grand gems I have, however, have been purchased and are part of planning ahead for future gear enchants. I thought I'd be using more of them by now, but I took the Deflect Arrows perk before knowing it was bugged and I've had to put improved enchants on hold for now to prevent further OP/balance issues.

The scarcity of creatures with Grand Souls in Skyrim is somewhat dissapointing.