I currently do something similar, but this is 2024 and someone in the vast Intuit software engineering department should be able to write code so that as PDF's are generated from different options within the software that they have unique file names so as to not overwrite each other.

No reason why an extension acceptance letter is overwritten by a return acceptance letter, or a subsequent amended return replaces the original.

This isn't rocket science.  The issue is programmers are not end users and don't understand the workflow.