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It sounds like you may be using "reserveOnOrder" inventory mode.  If so, for reserveOnOrder, the system has strict inventory checks. If the available quantity of a line item is insufficient, an "OutOfStock" error is returned. This prevents the creation or edit of the order. This restriction ensures that inventory levels remain accurate

To delete a line item from an order in this mode, you will need to use the order edits feature because there are financial implications to those changes.

If this doesn’t help address your concern, I’d invite you to open a ticket with our Support team so they can better understand your particular use case and provide additional guidance. 

Hi there ​@skktech, hope you had a great weekend.  Please, let us know how it went with the issue you were having. In case you need further support from us, we are here to help.