Lynn Pettis (another long time poster around here) pointed out there is a LOT more wrong with your query. I didn't bother to look past the hideous formatting but he ran it through a formatter. Once I did, my eyes started bleeding.

SELECT [Build1].dbo.TBL_TYPE_DEF.TYPE_NAME

,[Build1].dbo.TBL_INSTANCES.DOC_NAME

,[Build1].dbo.TBL_INSTANCES.DOC

,[Build1].dbo.TBL_INSTANCES.SEC

,[Build1].dbo.TBL_INSTANCES.VER

,[Build1].dbo.TBL_RELATIONSHIPS.JUSTIFICATION

FROM [Build1].dbo.TBL_INSTANCES

INNER JOIN [Build1].dbo.TBL_TYPE_DEF ON [Build1].dbo.TBL_INSTANCES.TYPE_ID = [Build1].dbo.TBL_TYPE_DEF.TYPE_ID

LEFT JOIN [Build1].dbo.TBL_RELATIONSHIPS ON [Build1].dbo.TBL_INSTANCES.DOC = [Build1].dbo.TBL_RELATIONSHIPS.PARENT_DOC

AND [Build1].dbo.TBL_INSTANCES.SEC = [Build1].dbo.TBL_RELATIONSHIPS.PARENT_SEC

AND [Build1].dbo.TBL_INSTANCES.VER = [Build1].dbo.TBL_RELATIONSHIPS.PARENT_VER

WHERE (

([Build1].dbo.TBL_INSTANCES.DOC + [Build1].dbo.TBL_INSTANCES.SEC + ISNULL(CONVERT(VARCHAR(10), [Build1].dbo.TBL_INSTANCES.VER), '')) NOT IN (

SELECT PARENT_DOC + PARENT_SEC + ISNULL(CONVERT(VARCHAR(10), PARENT_VER), '')

FROM [Build1].dbo.TBL_RELATIONSHIPS AS TBL_RELATIONSHIPS_1

WHERE (

(PARENT_DOC + PARENT_SEC + ISNULL(CONVERT(VARCHAR(10), PARENT_VER), '')) IN (

SELECT DOC + SEC + ISNULL(CONVERT(VARCHAR(10), VER), '')

FROM [Build1].dbo.TBL_INSTANCES AS TBL_INSTANCES_1

WHERE (

TYPE_ID IN (

SELECT TYPE_ID

FROM [Build1].dbo.TBL_TYPE_DEF AS TBL_TYPE_DEF_1

WHERE (

TYPE_ID NOT IN (

SELECT CHILD_TYPE

FROM [Build1].dbo.TBL_RELATIONSHIPS_ALLOWED

)

)

)

)

)

)

AND (CHILD_DOC IS NOT NULL)

)

)

AND (

[Build1].dbo.TBL_INSTANCES.TYPE_ID IN (

SELECT TYPE_ID

FROM [Build1].dbo.TBL_TYPE_DEF AS TBL_TYPE_DEF_1

WHERE (

TYPE_ID NOT IN (

SELECT CHILD_TYPE

FROM [Build1].dbo.TBL_RELATIONSHIPS_ALLOWED AS TBL_RELATIONSHIPS_ALLOWED_1

)

)

)

)

ORDER BY [Build1].dbo.TBL_TYPE_DEF.TYPE_ID

,DOC

,SEC

,VER

You need to use table aliases. IIRC using the full qualification in the select list has been deprecated. Just using aliases would increase the readability a lot. Then there are all the subqueries and column concatenation. You also need to avoid using sql keywords as object or column names. It makes things a lot tougher to work with.

The indexes and stats I mentioned are crucial for this to have a chance, but you could greatly improve this query. It probably needs a complete rewrite.