There was a similar discussion recently in the SD space (sorry, I could not locate it in the archive, but maybe you will have more luck than me).
Anyway, have a look at sap note 323048 - Sales order 'in process' although delivered+billed.
There is a report, which you can run to repair reference statuses in orders (you need to correct the customizing first).
Then follow the instructions in the note and run SDVBUK00.
Please test in a sandbox before you attempt to do that in your production environment.
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