For those who didn't know (I didn't until Dave told me), you can drag a CharacterAnimator scene straight into AfterEffects and it magically works with dynamic link. Except today! I just booted up my project after updating AfterEffects and all of the links are dead. I still have the original AE files, and it looks like I can rollback AE to a previous version (big thanks for making rollbacks easy, Adobe).
Right-clicking any file in AE should let you reload or replace footage. I just tried this with a project of mine, found the new paths with reload, and it worked. Upgrading can sometimes run into issues like this unfortunately.