Taking my cue from leeuniverse, I am going to share my 2 cents...
I am merging multiple libraries into my Plex library. When I find something I need to add, I copy it to a Staging folder on the computer hosting the Plex server, use Mp3Tag to make the tags consistent (sometimes this involves changing what is in the Staging folder, sometimes it involves changing what is already in the Plex library), and then move the files into the Plex library.
I would like to have one instance looking at the Staging directory, which needs to be refreshed all the time, and one instance looking at the Plex library that is large and slow to update.
I could probably live within one instance if there was a sort of folder browser pane that looked sort of like this:
If you click (or control + click) on a folder(s) it would add a filter (that applies before any filters you already have going) to filter to just that folder(s). If you select a folder(s) there should be a button to refresh that folder(s) without refreshing the others.
EDIT: There should be two buttons at the top of the pane: Refresh(refreshes only selected directories) and Refresh All.
To me, allowing multiple instances to run is the easier solution, though a folder browser is probably the more useful solution. Luckily I have access to Virtual Machine software, so I can run multiple instances, but that is a bunch of overhead and complexity that shouldn't be necessary. Another workaround would be to use multiple computers, preferably with some kind of Remote Access software, but again, that involves more overhead and complexity than necessary.