I often will have a long sequence and export one part, (mark IN, mark OUT) send it to AME and jump back to APP and mark a new in and out send the next section to AME and so on down the line. I have done this many times without issue.
The question, as I understood it was modifying the media in the sequence, editing, deleting clips in the sequence you just queued up for render.
I just tried this as a test, Paul is correct, you can modify a sequence, work on it, after you send it to render. My mistake there, I thought I ran into issues doing that in the past. I have always exercise great caution in not touching a sequence that was in queue to render or is rendering. Looks like you can.
I’ll still always make a copy personally.
Chris