Total Access Analyzer documents and parses the SQL to perform object cross-referencing. This works for standard Access queries, however the SQL parser is not entirely accurate for Pass-Through queries. Pass-Through queries are sent to SQL Server to run on the tables there. Consequently, the Microsoft Access database can't see those tables; so when Total Access Analyzer performs its cross-reference on the query's SQL it can’t cross-reference those tables correctly. In this case, ignore the cross-reference errors that are reported by Total Access Analyzer, but be sure to manually check to ensure that your Pass-Through queries are valid.
Note that if you have links to those tables (using the same names as how they are referenced in the pass-through query), then the SQL parser in Total Access Analyzer should resolve them.