Not able to remove Orchestration Instances from BizTalk Administration Console ?
If you are facing issues to Purge\Remove all Orchestration Instances in BizTalk, then there is one quick and dirty way to do it.
Execute the stored procedure msgbox_cleanup_logic.sql from the location $\Program Files\Microsoft BizTalk Server 2006\Schema
Note: Microsoft doesn’t recommend to use it on production server as this will delete all instances.
Preps Blog 