@tifsmo Unfortunately, there isn't a easy way to update it. But, if you take a look at the Blog, you will see that more frequent updates are part of the plan make by the Recalbox Team 🙂
It seems that you've found a solution to your save problem. What about if you create a symbolic link so BOTH discs can access the same file? Through SSH:
ln -s /recalbox/share/save/psx/Example_save_Disc1 /recalbox/share/save/psx/Example_save_Disc2
(replace ExampleSave, with the file name to match the disk, as you did in the first place. First file is the origin, second is the link you want to create).
I think it should work, and you will not need to deal with copies of a file that you can miss what is the most up-to-date.