Short answer: No. They can't tell that a given bullet was fired through a given silencer.
As Chris P pointed out, yes, they can match land and groove rifling from a given barrel to a given bullet.
Bullets never touch the inner parts of a silencer unless the thing uses “wipes,” and then the contact is merely incidental, not the kind that engraves a bullet with land and groove marks.
But suppose your silencer was run wet for maximum efficiency, and the dampener was oil or gel? That oil or gel would aerosolize upon firing. That could leave trace evidence.
As to eurodan49's information, I've never, ever heard about that and I'm interesting in reading. Any links? Pictures?