I reinstalled from scratch on the problem SSD, and it seems to be working now. I will monitor this and report back if it persists

Problem persists on Pulsar 9.2 Patron 4.1 Release.

Update: I upgraded to the v9.2 Patreon-3 release, and it still doesn't work. I tried with SN30 Pro and also the new 8bitdo Pro 2 controllers. I tried removing them from the recalbox.conf file, and pairing again.

I'm going to try a brand new install on a different SSD to see if that, somehow, magically works.

@Miga Are you using a USB 3.0 port or USB 2.1? I've had radio interference with the USB 3.0 ports before (on my PC) and it screwed with my wireless mouse and keyboard pretty bad. The fix I used (when I had no other options but a USB 3.0 port) is to use a USB 2.1 hub that's on a cable that moves the dongle physically away from the USB 3.0 port itself, and that seems to work.

8bitdo SN30 Pro controllers will pair, and work fine (even in-game), but once I restart the Raspberry Pi using the NESPi case's Reset button (using shutdown script, not sure if this matters, since it's just running a normal restart command) the controllers will no longer connect.

I have to remove the controllers from the recalbox.conf file and then re-pair them. Even then, sometimes that doesn't work.

Pulsar 9.1
Raspberry Pi 4
NESPi case (with shutdown/restart script)
8bitdo SN30 Pro controllers (latest firmware, just updated today to test if that was an issue, no change after update)

These controllers worked perfectly well before v9.1