I decided to create a “cheat sheet” with all my custom keyboard shortcuts by exporting to a ‘preferences.dat’ file. Sketchup had reported a problem with a file path preference setting, but I didn’t correct it at the time. While cleaning up the cheat sheet I noticed that several of my shortcuts were not included in the export file. I exported again, this time unchecking ‘File locations’ in the export options. The new export included the missing shortcuts. After correcting the file path issue, I tried exporting with both ‘Shortcuts’ and ‘File locations’ checked, and no shortcuts were missing (as far as I can tell).
So to anyone planning to export shortcuts to a new PC or new version - make sure all of your paths in ‘Preferences/Files’ are legitimate, or uncheck the ‘Files’ option, and check your results!
Hopefully posting this will put the issue on Trimble’s radar, as I didn’t see any obvious way to submit an official bug report.