Set save type to "Flash 1Mb" and hardware to "RTC", deselecting "Autodetect"
Load a modified copy of Pokemon Sapphire with a custom game code (PMSE)
Once the game starts to run, click "Save" in the Game Overrides window
Launch mGBA anew
Load the same ROM without setting up the overrides (using cmd+0)
Expected outcome: Modified Sapphire runs normally, with no in-game error messages regarding the 1M subcircuit board or the internal battery.
Game fails to load. Log indicates that it autodetected the save type as Flash 512kb, which is incorrect.
If I recompile the ROM with the boot-time flash check commented out, it will run but present the "1M subcircuit board is not installed" and "Internal battery has run dry" errors when progressing beyond the title screen.
The override.PMSE entry does exist in the file ~/.config/mgba/config.ini as expected, however it seems to be entirely unused by the emulator.
Can you upload the patch? I can't seem to reproduce using Pokémon Normal Version as the ROM hack (which has a code of PNV7). Also, make sure the override says savetype=FLASH1M and hardware=1. I know the override dialog can be a bit finicky and I'd like to fix that in 0.8.
While I cannot give you a patch with all the changes I made, I can supply an xDelta patch on Pokemon Sapphire US-EN v1.0 (SHA1: 3ccbbd45f8553c36463f13b938e833f652b793e4) that makes a minimal set of changes to reproduce the issue in mGBA: romcode.xdelta.gz