I think the problem is that to reset the identity column (which is what an autonumber Attribute is), you need to specify the table name between quotes, like this:
DBCC CHECKIDENT ('tablename', RESEED, 1)
I haven't tried it myself, but I would probably get the physical table name from the Entity System Entity, and create a SQL query with an Expand Inline Input Parameter that contains the physical table name including the single quotes.
Should do it.