Here a SQL Script to remove orphans from your BizTalk tracking. It sets an end date so they can be removed.
USE [biztalkDTADb] UPDATE [dbo].[dta_ServiceInstances] SET [dtEndTime] = GetUTCDate() WHERE dtEndTime is NULL AND [uidServiceInstanceId] NOT IN ( SELECT [uidInstanceID] FROM BizTalkMsgBoxDb.[dbo].[Instances] WITH (NOLOCK) UNION SELECT [StreamID] FROM BizTalkMsgBoxDb.[dbo].[TrackingData] WITH (NOLOCK) )