It’s funny how:
(a) over 9 years the Adobe CC price has shot up
and
(b) some issues still have not been resolved (hmmm…”Resolve”…that gives me an idea…)
I just had this exact same issue today, in July 2024: I have a ~7 minute edit with ~30 linked AE comps. I changed one of the comps in AE, and in PPro it looks perfect – all updated and nice. I sent the export to Media Encoder, where it sat slowly encoding for about half an hour. Imagine my joy, when I played it back, to find that rogue, old AE comp in there…even though this comp technically no longer exists anywhere…and how I had to embarrassingly and unprofessionally stall my client while I frantically fixed the problem. Thanks, Adobe.