This should be straightforward - fetch the top row from the customer table (ordered by LastUpdated) and any row from MessageTypeTrack which matches the filter criteria. I think the optimiser is confused by one of those filter criteria:

CONVERT(VARBINARY(8), cl.LocalLastUpdatedTS) < CONVERT(VARBINARY(8), c.DBTimeStamp)

which could lead to an expensive triangular join.

Bearing in mind that a query is a description of the result set, not a set of instructions to SQL Server as to how to accomplish the task, I think a better instruction for SQL Server would be something like this:

SELECT

c.ID,

c.LastUpdated,

c.DBTimeStamp,

c.AccountNumber,

oa.RecordID,

oa.LocalLastUpdatedTS,

c.PrimaryShipToID

FROM (

SELECT TOP 1

ID,

LastUpdated,

DBTimeStamp,

AccountNumber,

PrimaryShipToID

FROM dbo.Customer

ORDER BY LastUpdated ASC

) c

OUTER APPLY ( -- we don't care which - if any - row we get back

SELECT TOP 1

cl.RecordID,

cl.LocalLastUpdatedTS

FROM dbo.MessageTypeTrack cl

WHERE CONVERT(NVARCHAR(20), cl.RecordID) = c.ID

AND CONVERT(VARBINARY(8), cl.LocalLastUpdatedTS) < CONVERT(VARBINARY(8), c.DBTimeStamp)

AND cl.MessageType = 'Customer'

AND cl.MessageTypeVersion = '1.0'

) oa

Note that there are currently no indexes on either table to properly support the query - whichever way you choose to write it.

Give the query a try. It's not the only query which will work, there are a few options. Post up the actual execution plan of this query and your original as .sqlplan attachments (plans contain a ton of useful information). This will help folks figure out optimal index structure for you.