It's interesting because clearly the Master had access to a working Tardis to get him to the end of the universe, but if it was still functional why didn't he reclaim it when he had access to the Doctor's Tardis given that it probably worked a lot better!
Anyway, my thoughts.
1. The Master set the Tardis to remotely return to a much earlier time after dropping him off. This might make sense if the Daleks could track a Tardis (even at the end of the universe). The problem with this is that he clearly intended to become the Master again, see how annoyed he was with both himself and Chan-Tho for not opening the watch sooner.
2. The Tardis was recalled. Unlikely, I mean surely if the Timelords had this ability they'd have recalled the Doctor's years ago! If such a thing existed surely both the Doctor and the Master have it deactivated.
3. The Tardis was destroyed just after getting him to the end of the universe. This might be the most logical alternative, although...
4. Maybe the Tardis was destroyed in the intervening years he was Yana? Despite being near indestructable the universe was slowly collapsing and you get the impression humanity were constantly moving, retreating from the end of everything. Maybe his Tardis worked just fine, its just that the location he left it at didn't exist anymore?!