We don't know, but it seems like the store and any extra slots past the base 12 are linked. So as soon as the store comes back up, you'll get your slots back.
Let me never fall into the vulgar mistake of dreaming that I am persecuted whenever I am contradicted.
~Ralph Waldo Emerson
"I was just the one with the most unsolicited sombrero." - Traegus
Yeah, mine are vanished when the store is down but come back up normally when it's back online. Frustrating if you think of a great name during the outage, but not permanently a problem.
If we are to die, let us die like men. -- Patrick Cleburne
----------------------------------------------------------
The rule is that they must be loved. --Jayne Fynes-Clinton, Death of an Abandoned Dog
I submitted a ticket to them about this and they told me they were aware of the issue and working as fast as possible to fix it. 
My Global Chat Handle: @The Dreaming Shadow
Awesome Shadow. I haven't logged in yet but I really would like to start that toon lol.
10 50's To Date! Check out Titan Sentinel; it got my CoH presence synced online
Same problem here...but now Im missing two slots......and Im on 24 hours and it still isnt fixed.....
I know the in-game store is down, but both of my accounts paid-for slot's are relocked again. And not redeemable ones that weren't used, the ones that had already been opened up and labeled "Create A Character". Any idea why the store has been down for so long? I came up with a new character concept last night and I can't create it because my home server's first12 slots are full and my unlocked 5 are relocked again
.
10 50's To Date! Check out Titan Sentinel; it got my CoH presence synced online