I have two databases in one instance of SQL Server. In DB1 I have Table_1 and in DB2 I have a synonym that points to Table_1 in DB1. Whenever I want to clear out the contents of DB1.dbo.Table_1 from DB2 I just use:

DELETE TOP (100) PERCENT

FROM DB2.dbo.synonym_for_Table_1

This seems to work fine for me.