Since there is no error message posted I'd assume you need to set the collation for the MI alias used to compare against your subquery too:

and(RTRIM(LTRIM(MI.CLNT_MATT_CODE)) COLLATE SQL_Latin1_General_CP1_CI_AI NOT IN

(SELECT PROJECT_CD

FROM INT_AUX_PROJECT AS IAP

WHERE (DELETE_IND = 0)))