I have two SQL 2012 DBs - one has a table with a trigger, the other has a procedure that disables that trigger.
I've created a SSDT solution with 2 database projects, one for each database. For the second database I've added a Database reference pointing to the first database so that I can reference objects - however the line in my procedure:
ALTER TABLE [$(DbWithTrigger)].dbo.TblWithTrigger DISABLE TRIGGER MyTrigger
brings up the warning:
SQL71502 Procedure: [dbo].[CrossDbTriggerCall] has an unresolved reference to object [dbo].[MyTrigger].
I'm able to consistently reproduce this behaviour in Visual Studio 2012 SSDT and Visual Studio 2013 Ultimate.
Try
DISABLE TRIGGER [$(DbWithTrigger)].[dbo].[MyTrigger] on [$(DbWithTrigger)].[dbo].[TblWithTrigger];
in the SP. This should work.