If you’re worried about it, put all of your Pokemon into HOME before the transfer, but I’d bet that the OP left some details out and if you follow directions properly you will not lose anything in the process.
sounds like a great idea, like I literally have pokemon in my copy of violet that i've had with me for over 10 years from various different playthroughs, I would be so heartbroken if I lost them all durning that transfer
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If you’re worried about it, put all of your Pokemon into HOME before the transfer, but I’d bet that the OP left some details out and if you follow directions properly you will not lose anything in the process.