Thank you Naomi...this works. I am still trying to understand why the original statement stopped working...

;with cte As (select distinct EDP from  [AMSWHSERVER3\AMS].slotting.dbo.productinfo)

select CASE WHEN LTRIm(RTRIM(LEN(cUPCNo))) = 5 THEN '0'+ LTRIM(RTRIm(cUPCNo)) ELSE LTRIM(RTRIm(cUPCNo)) END as cUPCNo, 
		cSKUId, iForecastQty, cEDPNo, cMacsDescript, 
		cECometryVendorNo, cPVB, cProductTypeId, iWarehouseLocId, 
		cProductFamilyId, nCaseQty,
		CASE WHEN lBuyInCase = 1 THEN 'YES' ELSE 'NO' END as lBuyInCase
	from [BIZTALK\PRODUCTION1].MerchNew.dbo.m_newItem N 
                     LEFT JOIN CTE ON N.cEDPNo = cte.EDP
	where lSlottingUpload = 1 and CTE.EDP IS NULL
	And dSlottingUpload = '2009-06-17 13:35:15.000'