The Berry Glitch from Gen III Pokemon, How to fix it?

A while ago, I started playing my copy of Pokemon Ruby when something bizzare happened. A message saying "The internal battery has run dry. The game can be played. However, clock-based events will no longer occur."

I am still able to play the game but there are some in game events tha occur due to the time aren't working not because of this glitch. I looked up online on how to fix the problem and so far nothing has worked. So far I tried the Jirachi transfer from the bonus disc from Pokemon Colosseum and the Leafgreen Patch.

When Jirachi is transferred from the bonus disc to either Ruby or Sapphire, the berry program is updated. The thing is I downloaded Jirachi a long time ago before this glitch occured. I try to redownload but the disc won't let me.

I recently tried the Leafgreen patch but it says its unable to download the patch.

Are there any other rays to resolve this glitch?? If so, please tell me. I really want to be able to turn on the game and this message not to be there.