So I have found that in my case it was a directory ownership issue. I must have upset the permissions when adding roms to the folders (I do seem to recall renaming the Snes folder by accident and changing it back).
To solve the issue I ran the Retropie setup script and chose the option to ‘Reset ownership/permissions of /home/pi/Retropie/roms’.
After that I ran the ‘Start USB rom service’ option and all of my missing roms showed up on next reboot.
I am fairly new to Retropie and I am guessing that this must be a somewhat common problem if there is a dedicated script for fixing it, but searching the forums, this was the first post I found on the matter.
Hope the solution is this straightforward for everyone else having a similar issue.