In the season 3 premiere "If the Wheel is Fixed" Beka and Tyr return from the aliens' dimension. Dylan notices that his bone blades are missing.
As far as I'm aware there's never an in universe explanation given for them. Why did they suddenly vanish?
In-universe, they never really explained it, other than mentioning that it was something to do with the events of the "reboot".
Out of universe, it was largely because the actor (Keith Hamilton Cobb) continually complained about them and because they were a hassle to keep applying:
COBB: I was happy to see the blades go. I never liked them. They were a poor prosthetic made of rubber that you can actually see bending if you look closely at a couple of episodes. The way they chose to have him lose them was, I think, somewhat clumsily executed, but I was relieved to have them gone. I would have much preferred to have had him walk around with the broken remnants protruding from his forearms for an episode or two, with stories of how he had shattered them all smashing them repeatedly into the black, obsidian-like face of that alien whatever that had taken him captive. But instead, they just sort of turned up missing.
Right after the 'rays' were cut off when Harper reversed the machine they used to open the tunnel, at the end of that episode Dylan is talking with Tyre on the Command Deck, Tyre was removing his leather 'gauntlets' and raised his arm to show Dylan that his bone blades were gone. So, apparently, it is implied that whatever happened to him in that tunnel had something to do with his blades vanishing.
