I'm thinking that is a design flaw.  That said I only see one type of way to fix it.  You could get your reseller involved and have a custom done.  But if you are good with SQL you could tweak the SP that finds the items for pick.  I believe you'd want to change spsoGetIMAvailQty.  Probably not for the fainthearted though.  Plus you'd have to have some notification system that the order failed picking because of it.  So that would mean a log table and a view the pick person could look at.  Not that hard but a little time consuming.  If you have support you could call Sage and ask them what they think.

Good luck.

The user is given a warning message when they attempt to create the pick list for a partial shipment when the customer has the Ship Complete flag selected.   They are able however to proceed with printing the pick list if they choose.  They will not be able to commit the shipment however. (Note - if you select the option for Ship Complete in Maintain Customer Classes, it will NOT be updated to existing customers - these would need to be updated via Maintain Customers.)

Jenny

To get around this issue in 7.2, we actually generate a Knowledgesync alert to the updateuser's email address and the salesperson's email address alerting them that they need to fix it. The alert runs every minute and check to see if there are any orders meeting this criteria.

The reason we can get away with doing this though is that we batch ALL of our picks and they get funneled through one team in which that is all that they do. Our batched picks can take as long as 45 minutes to an hour to run, So this gives the salespeople necessary time to go in and fix some things on an order, also...