As soon as I wrote this out I had an idea: I doublechecked my framerates and my AE comp and the Premiere timelines didn't match. As soon as I interpreted the AE comp to match the timeline, the footage popped back on and everything rendered correctly. I'm surprised that an update would break something like this, but at least there's a workaround for now.
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It's possible the update didn't break it, but actually fixed it. There was a bug in previous versions that treated 23.976 pretty much the same as 24, even though the two are different. The 4.2 update corrected that.
That could very well be the issue, my AE files were setup as 29.97 and Premiere was 23.976. Syncing them up made it all magically work together. Thanks!