I think @SkritterJake might have a more ambitious reply in the making, but in the meantime, I’ll share what I do. I also see that you found a solution that works for you, but I thought I’d share my experience in case other users read this. My situation is not identical to yours, but it’s close enough that it might help!
When I started using Skritter again for my own learning (rather than for testing purposes), I had accumulated a due queue of somewhere around 5000 characters. I only study writing and only single characters, so that’s a serious pile, drawn from roughly ten different decks.
What I do to avoid the problems you mention is to go to normal review, then select only certain decks to review from. Ignore the large due counter on the dashboard for now. When you start, you select only one deck. You work your way through that deck until you’ve depleted the due cards in it. Then keep going with the other decks. Since you’re only working actively on catching up on one deck at a time, things you get wrong will show up immediately in the next session. You can also study and learn new things from other lists by studying them and then including them by including those lists when selecting which lists to review.
I’ve been doing this for a month or two now and I’m down to about 2000 due, most of them in two specific decks that contain a lot of fairly rare characters. When I review, I select everything but those two, which makes Skritter work like you want. There is no way to inactivate decks, but by always doing selecting reviewing, you achieve the same result (it would be great if this was easier to do, but it does at least work)!
Personally when the list is too large I just press enter all the time, it’s quite boring to do but in 1 or 2h should be clear
I strongly advice against doing this, unless you have spent significant time writing characters outside Skritter. You’re effectively telling the algorithm that “hey, even though I haven’t studied this for a year, I still know it well”, which will push it out even farther into the future. If your only goal is to remove the queue, this obviously does the trick, but I assume that the goal is to still maintain the knowledge that these characters and words represent, so simply marking them all as correct is not a very good idea.