Praeter (played by Peter Dinkeldge) has a bunch of high level trophies from Dexter's hey day in Miami.

But it's not just that he's a collector, he wants to understand everything and would pour thru everything. If he got an agent to hand over something as irreplaceable and important as the slides, it's a safe assumption he's read everything the FBI has.

Dexter would be of huge interest, because Praeter could connect Dex to BHB, Trinity thru his wife, and with how big of a deal they made about orphanage donations, I bet he knew Dex and the Ice Truck killer were brothers. And pretty sure Deb dating the Ice Truck Killer was public knowledge after, he'd know that too.

Charlie (Uma Thurman) has shown that they don't hesitate to pick up evidence and follow threads better than the police. So putting the dots together on Dexter is pretty likely.

Praeter could have been 100% sure Dexter was the Bay Harbour Butcher. But also sure he was dead and gone.

Until Batista pulled the death paperwork and officially brought Dexter back to life. Now, Praeter may not have heard of that, maybe he did by having a flag for news alerts or something. It would make sense because he'd have a long list of names/cases he wants to know if anything happened.

But even if he didn't. A few weeks later the BHB's body disposal hallmark shows up in NYC, and no matter who Praeter expected, he saw and recognized on sight Dexter Morgan, the Bay Harbor Butcher.

So he immediately showed him the three things he would care the most about and Dexter couldn't hold it together.

Edit:

And since he'd obviously be aware of how Justin's body was disposed of and how that was Dexter, he's going to know that was a frame job.

The other killer disappearing is also going to make it pretty obvious to Praeter that Dexter is killing them all.