QBs does not let you actually Delete any accounts that have transactions in them.  It only lets you make them Inactive (aka Hide them).  And you're correct, even through it's Inactive, the Acct still shows up in some reports.

So how many transactions are there in the account you want to get rid of?  Your best bet is to Delete them and then QBs will allow you to Delete that Acct.  You may want to compare the transactions as your deleting them just to make sure you've got them all.  But when you Reconcile you'll catch any missing entries too, so comparing is just belts and suspenders I guess.