I suspect it'll just check for the confirmation of the first transaction. If they aren't included in the same block, it may just pass the second. However, it is nowhere stated that you have to send your amount in one transaction. There's no answer in FAQ, so only @ChipMixer can enlighten us.

The real question is:  Why do you want to send multiple transactions funding the same ChipMixer address? Why not redoing the procedure with a new deposit address?