The dynamic link between CA and AE needs fixing
If the Dynamic link gets corrupted it makes you relink every scene when After Effects opens. But there's a big problem - the order of the scenes is NOT the order they appear in After effects, so you have no way of knowing which order to relink them in. This should be fixed. Please tell the user which scene After Effects is looking for in the Character Animator file when the Dynamic Link window is up.
Dan Tull commented
Which versions of the apps are you using? We had an issue where certain operations in Character Animator would invalidate the internal IDs used to identify scenes for dynamic link (thus breaking the links), but I think that was fixed quite a while ago. I'll have to do a spot check that the issue has not been re-introduced.
Do you know what kind of change is causing those links to break?