The "bad" file was issued a Ticket to notify corrections needed. IF you corrected the errors, you need to re-deliver your book using the same iTunes Producer vendor ID. Dont use Publish in iBA, open the original ITMSP and re-deliver.
IF you started a second Publish with a different vendor ID it seems that the ISBN is your "association" problem.
Are you aware that Apple dropped the ISBN requirement for iBooks Author produced eBooks some time ago.
If you are distributing the same book away from Apple, then you obviously need to comply with whatever rules apply
Delete/Overwrite: In reality, what you submit to the review team cannot be deleted and as far as I know the ticket is not cancelled unless your correct the errors and re-submit.
A book once accepted into the store, can never be deleted as such, but you can remove it from the store using your iTunes Connect account, select the book, and remove ALL selling rights worldwide.
After that if you produce an identical book and start a new delivery with a new vendor ID, it is OK BUT although you can hide the first book from sales... the ISBN number is locked into that book.