Orphaned shares after transferring to another account using "remove shares"

My problem is similar but different. I "remove" shares. Alternatively, I transfer them to another account and it automatically creates matching remove and add transactions in the relevant accounts, and it even asks me to specify a lot. But then, in the account the shares were transferred out of, I now have orphaned shares, about which I'm asked to create a transaction and/or estimate a cost basis. This makes no sense.