When I have a downloaded transaction that I have accounted for in some other way, and that transaction is likely to be downloaded again, I Void the transaction rather than Delete. That way Money realizes it has that transaction already, and does not add an entry to the register.
This comes about if I enter a split, such as a 3:2 split, that results in a fractional share. I will let Money generate a Sell of the fraction. Then when the CIL (cash in lieu) comes in, I void that. If I deleted, I think the CIL would come back in, because I overlap my download date ranges. I also note the amount of the CIL, and go back and modify that Sell, replacing my estimated sell price. Failing to notice the incoming CIL is what I often track down any balance mismatches.