I don't know if this kind of thing still gets discussed here but I wanted to report an issue I am having with the new version of AE in the hope that it might help someone else (and to see if anyone else is seeing the issue).
I am seeing behavior in the new version in which projects that contain PNG sequences seem to lose those sequences, giving this dialog for every g..d... piece of media. I can cause the error by simply tabbing to another app and then back into AE. Note that projects open fine with all media and if you dismiss these multiple warning dialogs, everything works fine (of course for some projects, that can be hundreds of dialogs).
The error seems to disappear if you turn off Auto Footage Reload.
Windows 10 Fall Creators Up to date 256GB Ram All SSD or m.2 Nvida 2 Titan X Pascals 2 1080's.