So, looking for a suggestion from someone who may have been in a similar situation.

For a while now I've been slowing working my way to the end of the RtK book while doing sentences and taking classes. Needless to say, kanji had taken a backburner. However, I always kept up with my reviews. However, I noticed after a while that old cards hadn't popped up in a very long time. I went and checked, and sure enough the browser in Anki showed me a ton of cards due 9 months prior, but hadn't popped up. So I asked for advice on the Anki forums, and did a DB check and now I have over 1000 failed cards (automatically placed there) and I find it very hard to remember ANY of them.

So, my question is, to anyone this has unfortunately happened to, or anyone who has an opinion: Should I just go through the failed ones, or reboot the deck and just start over and review anyone I can't remember? What would be quicker? It's looking like the first option, but that just makes me really depressed.

Any advice?

That's rough. If you weren't paying much attention + haven't studied them in ages + never finished RTK in the first place, I might recommend just starting over. Otherwise I'd say just treat them as failed cards.

Yeah I tried to go through about 50 of the failed ones and found myself really struggling to recall them, as they were all the ones that should have been reviewed 10 months ago. I think I remembered 4 of the 50 or so. So looks like I might be starting over. Should be real quick to get back, no?

I think you'll find they're in their latently somewhere... so it should be easier to re-learn them and have them stick fairly well... at least thats what I found for ones that I forgot after a few months.

I've been there (more than once, actually). I would never recommend starting over, but rather develop a system for working through them. Start by setting Anki to not show failed cards for a while, say 8 hours (this is a good idea anyways). Then find a pace for working your way through and make a game of it. But whatever you do, don't turn it into a race. Just go at whatever pace is natual and you'll eventually get them done. You might find this thread interesting:

http://forum.koohii.com/showthread.php?tid=2632

I found myself in somewhat similar situation a few months ago.

From between December 20 - Jan 20 I covered RtK 1000~2500. As a result I burned out, so I took a 1 week break, which led to at 2 week break, which lead to a 2 month break.

When I came back in May, virtually all my cards on Rev the Kanji were expired. I exported all of them into Anki, and over the next few days I reviewed all of RtK 1 cards. I passed something like 750/2042.

After that, I starting adding my failed cards from the beginning of RtK. I reviewed my stories, and basically repeated the RtK process, minus the cards I knew. However, the second time around it was a piece of cake. Now, I can know 90-95% and my Anki RtK reviews are at about 20 per day.

As others said, re-learning kanji you knew before is usually a piece of cake.

My recommendation is to suspend all of the cards that are due, and then un-suspend them in batches of say 50-100 (in RTK order). Review them to see which ones you forgot, then spend time learning those. Once you've cleared them unsuspend some more and repeat.

Re-learning is so simpo. There's even clinical support for it: http://forum.koohii.com/showthread.php?tid=2157