Sounds like it has been tracked and costed (per the WIP In-process posting function) already and the stock journal has reflected the WIP and RM inventory accounts. I am not sure that anything could be done at this point as don't think that there is a utility function to reverse work order postings. You may have to reverse the posting in the journal entry and then either i) re-issue a new work order with a new BOM and made ajdustments or ii) update the work order header table MFGHEAD to status 1 (open) and MFGHEADTRK via back-end (although this is probably not recommended).

This is the workaround posted in the KB.  We've had this same issue as well.

• The order must be Completed and Closed.
• This will require entering at least one tracking record.
• Possible workaround
  1. Go to the WO record, Operation tab and Exclude all operations except one.
  2. Go to Manufacturing, Production Tracking, Production Tracking
  3. Create a New Entry and select the work order.
  4. Only select Operations Tracking. Make sure to zero out fields like Actual run-time so the cost is calculated as zero and no WIP variances are created when the WO is closed and costed.
  5. In the Total Actual Quantity field, enter '1' or the total quantity.
  6. In the Total Rejected Quantity field, enter '1' or leave it blank.
  7. Create the record.  
  8. Notice the WIP cost inquiry shows zero in Variance (%) column and all other fields are blank (in the Totals tab)
  9. Now you have the option to Complete, Close, and Cost the order. No GL entry will get created as expected.

I'm having a similar issue today.  From the looks of it, the finished product was tracked on, but then the tracking was deleted.  I don't have a record for it, but it was costed so the tracking shows up twice in the stojou table (one for a positive addition, and the second line is a negative).  We get the same error though.  What should we do?