Okay, so upon further inspection of the roms. (All of them, not just the eShop one)
I've come to the conclusion that there is no working patch for SMA4 on AGB_FIRM at ALL, the one posted to the GBA 2 CIA topic is broken as well, even when applied to the correct rom and everything.
Even the ones that "work" have a problem with corruption in one way or another.
If I save the same save twice in the standard mode, it will write to the second file instead of the first and this causes the corruption and save data loss.
No idea how to fix it either. One time when loading a save it threw up the "Save data is corrupt" error again at me in the file select screen.
And this is on the patch that was from the GBA to CIA topic applied to the appropriate rom the patch was made for.
I did take the time to make a version of this patch to be applied to the eShop version of the rom (After you apply the eShop version IPS) too, actually. It edits the correct bytes to make a "Fixed" version of the eShop rom. But as I've stated, this doesn't actually fix the issue entirely. If you do choose to play the game this way, I strongly recommend you don't use quick saves. (IE, don't pause and pick Save & Quit)
So to be clear, you apply this patch AFTER the eShop patch, and when you generate a footer for the rom using the footer tool, do not change anything.