Forgive me if this has been said before or if there's already a work around. Basically, I use combination geological/gravitational survey ships with primary orders of 'Survey Next Five System Bodies' and secondary default orders of 'Survey Next Three System Locations'. This works fine for surveying system bodies, but once it runs out it triggers an 'orders not possible' message every time it finishes surveying three JP Survey locations.
My suggestion is just to make it so that if a ship cannot perform its primary default orders then have it perform its secondary default orders, and shunt the secondary orders into the primary slot so that it doesn't display a 'Cannot Perform Orders' message every few days. Of course this might conflict with some other forms of default orders I'm not thinking of, so perhaps add a check box for this option.
This is working as intended. I am not sure that swapping the default orders around would be a good idea. For example, if someone had Survey Next System Body as the primary order and Move to Entry jump point as the secondary, you would never want those to be reversed. As to the 'orders not possible' event, it needs to be an interrupt so you can deal with it if necessary. It isn't really possible to not issue the event when there is a secondary order for several reasons. The default orders code doesn't know whether it is handling a primary or secondary and even if it did know the order was a primary, it wouldn't know at that point whether there was a secondary order involved and if that would be possible. It is all handled in a linear way.
Steve