I have not been having problems at all replacing a composition in After Effects. I understand that workflow.
However, when you dynamic link between Premiere and After Effects, it imports all the footage with the trimmed in and out points as separate layers. As in, the whole length of the clip is visible, but only the in and out point is enabled. Is there way to import a project from Premiere without the disabled section of the clip so I can replace the clip with a colored clip with only 1 second handles?