I had a well-known issue where I masked something in a pre-comp and then time-remapped the pre-comp and the mask became out of sync.
The logical solution to this was to create proxy file of the pre-comp, which of course renders it out. This appeared to solve the problem as predicted when I looked through my final timeline. However, when I came to render out the final timeline the mask became out of sync again.
AE defaults to NOT using proxies for final renders.
When you add your final comp to the Render Queue, open the item's Render Settings and change Proxy Use from "Use No Proxies" to "Use All Proxies" or "Use Comp Proxies."
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