I had this issue with MSMoney some years ago. I had an old credit card account that was closed out and I deleted that account. When I did that, every EFT to that account also disappeared from my checking account register, throwing the whole register off!!
While it is not an urgent question (since it appears all my closed accounts did not convert into Quicken), would the same thing happen in Quicken if I deleted an account which I had paid by EFT from checking?
TIA Jim