No you won't lose you save files. If you did, I'd be extremely surprised. Just make sure to be gentle and try not to touch any electrical components (if any) that are exposed. If there is any corrosion from the old batteries coloured, blue, blue/green or yellow, mix some bi-carbonate soda with hot water, preferably boiling and wipe it over the areas with the corrosion lightly. It might be best to use an earbud. And make sure you use it sparingly or you'll totally ruin the GBA altogether, basically don't flood it with the bi-carb/water mix.
EDIT: Should also mention, that if any electricals are exposed (wires etc) don't try to clean any battery corrosion using the above method. The battery acid corrosion shouldn't affect the GBA entirely unless the contacts are completely covered with it, so you don't necessarily have to clean it. If there is anything exposed that shouldn't be, I'd highly recommend getting someone who has experience in electricals to do it for you. Generally with older consoles, handhelds etc, disturbing them too much can cause them to malfunction.
If the internal battery has 'run dry', the games time won't progress correctly, and won't allow you to do time based events, like berries. You can replace the battery, but I'm not sure about how one would do so.
XerX wrote:If the internal battery has 'run dry', the games time won't progress correctly, and won't allow you to do time based events, like berries. You can replace the battery, but I'm not sure about how one would do so.
The game will still play and save fine.
I think if you replace the battery the entire cartridge is now considered void and if you try to sell it in the future you might run into some problems because it's technically not the original game.
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Technically, it's no longer the original game once the battery runs dry because you no longer get the game's full experience. So... people will do what they must. I doubt anyone would mind buying a refurbished game as long as they were guaranteed it would work, anyway.