@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.