I have the following suggestions:
1. Based on current rule in say, Terr A, if the accounts in question are assigned to Terr A, but your requirement is that these accounts should be in fact be in say, Terr B; then you may want to add these accounts to Terr B using "Account Exceptions". Accounts under "Exceptions" take precedence over the Accounts in a rule.
2. If there are accounts that you want to delete, because they are getting assigned to the territories that they should not be under; you may create a dummy territory with a rule adding all those accounts you do not want to see under any other territory as account exceptions. In this manner your master data stays intact. (I would not imagine you really want to delete accounts).
Hope this works for you.