Have had this problem on numerous occasions on and off realms where minecarts that have left running in an automated redstone system will randomly despawn. The minecarts in question are usually hopper minecarts running on rails with only 1 block height to move around in. Doesn't seem to be any pattern to when this happens and I have had to replace several of them.
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Thank you for your report!
We're tracking this issue in MCPE-21416, so this ticket is being resolved and linked as a duplicate.
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