I think there are different files for the GUI and the real "users" file of freeRADIUS.
I think you can sync the users files of both freeRADIUS and it will work but it will not show up in the GUI.
And like you said - after doing any changes on the freeRADIUS GUI all changes you did before will get lost.
I think you'll have to find the file which is responsible for the freeRADIUS GUI and sync this file, too.
If you found any solution, please let me know!