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I bought some copies of Gen 3 but the batteries are all dead. I plan on changing the battery, but I’m not sure how that will affect the berry growth. If I plant them now, will they grow after I change the battery? Should I leave the berries? Or would picking and holding onto them for later be the best option?

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This might help answer your question
What part of your question is not already answered by that other question's answer?
Should I leave the berries be, pick them, and how long would they take to grow? Would planting them after the batteries are replaced still require waiting since the cartidge was dead when I started the save? Or would it just start from 0-0-2000 again?

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If I plant them now, will they grow after I change the battery?

The RTC and the save data timestamp would be different, causing the berries not to grow because the RTC would be at 1/1/2000.

Should I leave the berries? Or would picking and holding onto them for later be the best option?

You can pick the berries if you want, that won't affect anything, you just can't grow more for a while after you pick them.

Berries will not grow on a game with a restored battery unless you let the game sit for as long as your save data has been active. You said this number is 5 days, so that means your save data's timestamp is currently 1/6/2000, and your RTC once you replace it will be 1/1/2000. (Nor your save data or your RTC know what year it is, and it didn't know it back in 2002 when these games came out either.) Your RTC currently is void because your battery is dead.

The only way for you to grow berries in this scenario is to replace the battery and then wait 5 days until your RTC catches up with your save data and updates it, allowing berries to be grown again.

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Why does it need to sit for 22 years to catch up? It’s a gameboy; it doesn’t know what year it is.

I don’t think your answer is correct and you don’t have a source added or any reasoning for thinking this. The save file has been active for 5 days, so wouldn’t it just need 5 days to catch up?

The answer in the previous question was for if the battery died *during* the save file, and mine hasn’t. It was dead from the beginning

And this doesn’t answer if it’ll be any different if/how I plant the berries
Let me get the order of events straight then, ok?

You bought dead games with deleted or never started save files. You started the game with a dead battery and progressed until you reached a berry plant. You are now deciding whether to replace the battery or not and whether to pick the berries or not?

Is that correct?
No. I bought game with dead battery and started the save like 5 days ago. The rest of your assumption is correct. I am currently waiting to change the battery before picking the berry, but I am unsure if I should pick them before changing the battery, or after, and how many days it would take if I changed the battery before planting, if at all
Edited! I thought originally you bought games with save files active.