Well it didn't quite work this morning but I realised that the box needed to actually be on for EPG Export to actually do what it needed to do, so I set up a test for 9am with the box on and that worked fine.
I manually ran the script to move the exported file to my NAS and then manually updated the TV Guide data in Jellyfin and all seemed good - it even kept the recordings I'd set.
Set up one more test for an EPG Export at 10am, cron job to run the script at 10:15am and Jellyfin to update guide data at 10:30am and everything worked so I've adjusted the times back to daily after 6am so hopefully that should solve the main problem.
My only other possible issue will likely be the ongoing accuracy of the EPG Date for the purposes of series linking things.
