There seem to be two possible ways to do this. I don’t know which is better. So I’ll save my present development folder in case it doesn’t work out. One way is to add another field in my GEDCOMs list that indicates a physical GEDCOM number that will not change. The other way is to make the changes to the Instant Organize and Navigation history lists whenever a GEDCOM is deleted or reordered in the GEDCOMs list.
Adding the physical GEDCOM number seems more appealing, since adding a previously deleted GEDCOM would enable restoration of the history lists. So I’ll try that first.