The easiest way to clear these is to convert the "unbilled expenses" to invoices, then zero out the quantities invoiced.  It has no impact on either revenue nor inventory levels (nor your balance sheet).  There is also a much faster bonus in that you can add in all pending unbilled expenses for the customer in one transaction.

My business has over 4000 sku's and anything that was listed as an "inactive" item in QB desk top shows as a "deleted" item in QBO.  The designation is essentially the same but confusing when seeing the word "deleted" next to the sku.  All items that were inactive/deleted had to be made active again to clear the charges off.

As far as invoicing a zero amount invoice, the software only sees the unbilled expense as converted to an invoice, thus closing out the open transaction.  the dollar amount has no bearing on the ability to clear them out this way.