I just had an idea, and checked how many jobs were stored on the Duet (and how large they were) and found that once I cleared out a good few that were old data, everything displays.
That said, the PanelDue was not displaying quite a few files, and a wide variety of ages and sizes were invisible for some reason.
After purging ~150-200MB of gcode, everything appears to show on the PanelDue, including some I thought I'd deleted from the Duet, and were still stored on it.
As the title says, the only common thread I can find is that I recently started using PrusaSlicer, and the files that I slice in it do not show up on the files list on the PanelDue, but all the files sliced in S3D show up normally.
Looking in the Web Control Interface, they are all present, and in order that I uploaded them, most recent first, the PrusaSlicer files most recently.
They print as expected, if managed from a PC or even my phone. I just can't see them on the Panel Due.
Firmware: RepRapFirmware for Duet 2 WiFi/Ethernet 3.1.1 (2020-05-19b2)
Duet WiFi Server Version: 1.23
PanelDue v1, 4.3", Firmware 1.23.2
I can update the display to v 1.24, but I'm not seeing anything that looks applicable in the update notes, so I didn't want to push my luck and potentially have a failure if it's unrelated.