so it sounds like you are creating a new order entry for the invoice which goes awry not reprinting it.

it posts to the general ledger but not the customers account.

if this is the case you could try this.

create a general ledger account called "suspense account" as a expense account.

create a customer account called "suspense"

once you have created the new invoice go to the customer's account and copy it as a credit invoice.

go into order entry and open it changing the name to the new suspense a/r account and save it.

this will clear the unseen transaction in the g/l accounts and should put the inventory back into stock.

go into the a/r suspense account and do a debit entry using the new g/l  suspense account once done link the entries.

at some point in time if you wish to clear the g/l account you will have to a one-sided entry.

look up "Answer ID 20267 in the Knowledgebase" to see how to do it.