Hi @rigojr-hotmail-c
This sort of thing happens all the time here!
In Company A QBO, enter the outgoing payment as a Cheque/Check to a Loan account (inter-company / Employee Loans - it doesn't matter too much as you're going to repay it straightaway). Enter the Incoming Payment as a Deposit to the same Loan account. The Bank Register is now correct & the Loan account has been zeroed.
In Company B QBO, you already have the Bill. Enter the (inter-company) outgoing payment using Bill Payment as usual but add a Memo to show what's been done (just in case you forget at a later date).
Hope this helps.
