It shouldn't make a difference because the battery is not powering the SD card. The battery on the PCB is used to power the RTC and the SRAM.
When the savegame is saved to the SD card (I am uncertain if the EDGBA X5 does that on boot or when loading a game), the battery doesn't play any role in keeping the savegames on the card.
That being said, the battery should last longer than three months, a few years should be the expected time for the battery to run dry (probably close to a decade, really)