While Modify a BizTalk Application Resource recently something went wrong, leaving BizTalk in a strange state.
When opening the BizTalk Server Administration Console the following message would be displayed:
Schema referenced by Map 'NNA.DBS.BizTalk.LOB.Maps.ProcessPartShipmentBPDToStar' has been deleted. The local, cached version of the BizTalk Server group configuration is out of date. You must refresh the BizTalk Server group configuration before making further changes. (Microsoft.BizTalk.Administration.SnapIn)
The problem with this was that any attempt to refresh the BizTalk group in the console failed.
I also tried such things as service and server restarts but nothing so simple worked(If you stop the host instance, you can still expend the BizTalk Applications tree).
Following various leads lead me to look at the bt_mapspec table in the BizTalkMgmtDb database. Here I saw that, there was an entry for the map that the error was reporting on.
Deleting this entry allowed the group to be refreshed and the undeployment and deployment of updated applications have since been working without any problems.
DELETE FROM bt_mapspec WHERE itemid = xxx (better copy the whole row first in case of any error)
Note:
Before you Modify a Schema resource, be careful check the related Map resource. If a map reference to a schema removed in you Schema resource, the error happens. To avoid this, you have to remove the Map first, then modify the schema, then add the Map.