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No. There's a huge different between NDS's wifi multiboot and running a flash card. From a echnical point of veiw, the data sent via wifi should always be the same.Trying to send a game from a flashed DS/flash card to a retail DS ought to be pretty much the same as trying to run a flash cartridge without a passcard. The DS should refuse to run it. Those few games that do work probably send themselves in a different way from the rest.
The only potential problem I can imagine is synching; like if the game is running laggy on a backup utility.