The EZ3 had such functionality at one point. Being hardware based there are timing issues (you have to stop the game to do it rather than reach in and grab it from an emulator with the emulator never knowing anything happened) and I think some write only stuff (the read only stuff mostly troubles the DS with 3d but I will have to look for the GBA).
Whether that is viable for the various pieces of open source that EZFlash have released ( https://github.com/ez-flash ) I don't know as some things might take, or at least work 100x better with, the cart itself doing stuff.
You could probably hack together things on a game by game basis as well -- change the save to a ridiculously large one, pause the game and pipe in the data to it, reverse the process where necessary.
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