Unfortunately, I do not think so. It just means that berries can no longer grow and the tide will no longer change in Shoal Cave. You can still play it other than that. They fixed this glitch in Emerald version.
Actually, I think there was also a patch for this glitch if you were to download Jirachi from the Colosseum bonus disk, but I would have to double check on that.
You are thinking of the berry glitch, this is something different. Same effect, but the way to fix it is to replace the internal battery, which has died.
So I guess, the only thing you can do now is to replace the internal battery or get a new game
Actually there is a way to fix the Berry Glitch, you would need another GameBoy Advance, a link cable and a cartridge of either FR or LG. To perform this, you need to turn on the other GBA with the FRLG in and I think as you turn on, you're supposed to hold Select/Start and it takes you to this menu. The menu then tells you to link the other GBA w/ your Ruby and there the connection actually fixes the problem.
Hope this helps (in case you have another GBA...)
Indeed. Poor old GSC had the save file tied to the battery; RSE just loses a few minor features.i understand, at least the game is still playable