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The only two examples that I've seen given are the fact that berries don't grow and the Shoal Cave doesn't change its tide. I haven't been able to find a complete list of all negative effects anywhere.
I'm considering changing the battery but so far the berries and the cave aren't enough to make me want to do it, but I'm thinking the other effects might.

Thanks in advance!

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It just disables all time-based events, If I recall

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It affects time-based events, just like the Berry Glitch, except it isn't fixable.
Eevee Happyvolution locked into one or the other
Berry growth stops
Daily freebie Berries
Weekly Frustration/Return TM giveaway
Lilycove lottery
Random TV shows
Secret Base Battles
Shoal Cave is locked at either High or Low Tide meaning you cannot make Shell Bells and if it is locked in high, you cannot access the lowest floor to get Snorunt or the NeverMeltIce- RaikouTCG

In addition, Mirage Island and the Feebas spots are fixed into their current state and positions.
Some of those might be considered major, but none of them really prevent you from progressing through the game.

Source

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Awesome, thank you so much!
Glad I could help
It also gives you a fixed RNG seed, which has several implications for shiny hunting and RNG abuse.
Info on fixed seed: https://youtu.be/3nU2SV4hyng