I render out a lot of image sequences at work, b/c if you have a small change in the middle of an animation with lots of layers and effects, overwriting a few frames is a lot faster than a whole mp4. It drives me crazy that I can't patch up a few frames in the middle of a sequence with media encoder. I have to take the time to let AE render them, or downsave to another version which is inefficient.
Why isn't there the option of using the same frames numbers as the after effects comp that's been exported? I officially request this option in future updates. Unless anyone knows of a work around? I haven't been able to find one.
Mp4's use time code, not frame numbers. So AME can't put frame numbers on them. That's life.
It should be a fairly easy task to make changes in AE, render out the modified frames in a different folder, then do a copy & replace to the original folder. You're set to make the whole thing again in AME if you wish.