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)
)