well, i would need to fully explore that cave near the 7th gym's city and grow berries, among other few time based events...so?
is there a known patch or is it hopeless
If this happens in all the games you need to save in, then yes your 3-in-1 battery has run dry. It happened to mine a few years ago. There's really only two things you can do. You can either buy a 3-in-1 or buy a new battery and replace it yourself. There are various tutorials for the latter option.
"The internal battery has run dry" is the error, right? That would mean the real-time clock isn't working. Try this thread. If it doesn't help, you could try googling "Pokemon VERSION real time clock fix" or something similar.
well,googling helped a lot...but you are right, it's the game's problem
i have heard that the gba emulator has the rtc option, so do you guys think i would be able to get my game in the emulator for those parts only, and then back to my r4?
Few things to sort out
1) There is RTC Patch for Ruby and Sapphire versions of Pokemon game, there is no patch for Emerald version (unless something changed...)
2) Moving save between VBA and EZ 3-in-1 is as easy as eating bread, You just move save file in and out as it is, no conversion, no pain
3) Theoretically any game that requires clock could be patched that way as Ruby/Sapphire but someone would need to create such patch (EXE 4.5 T_T)
Don't bother changing the battery. The ONLY time you'll know that your battery TRULY has run dry is when you lose your savegame. That indicator is useless. GBATA can patch Pokemon ROMs' clocks to tick when the game is running, but cannot do so for Emerald. I have looked far and wide and to the best of my knowledge there is no such patch for Emerald. Yes you should be able to export the save to emulator in order to have the clock running there.
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Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)