It just occured to me exactly the way Arthur Petrelli's power actually works. But, first, let's look at Sylar and Peter's powers:
Sylar's ACTUAL power is to understand how other people's power works (the same way he fixes the watches). He needs to open their skull cavity to see their brain to access what portion of their brain activates each ability. Once he understands this, he's able to access each of the same abilities himself. This explains also why he may not always exhibit ALL of his abilities at once (ala Ultra Boy, who could only access a single power at a time (if he wants to be strong he can't be invulnerable, etc.). Put simply, it's possible with Sylar that until he is proficient with an ability he can not always access it immediately but takes time to think about it (that's why his go to power is the telekinesis because he's PRACTICED that one and thankfully for him, the Claire/Wolverine healing factor is apparently an ability that functions like breathing and is an automatic neural/nerve function that happens unconsciously.
Peter's power is a little different. His works just as unconsciously as Claire's. He is seemingly automatically grabbing abilities from those in his proximity (though, again, he may not necessarily know his entire catalog of abilities...he did not know until only a few episodes ago that his prophetic dreams came from his mother). Again, Peter has to learn to use the abilities he has and KNOW what he has (though Sylar's abilities added to that mix...the understanding how powers work...may help him figure out what has happened to him with his father).
Arthur's power, I think, may be more like Rogue, though I doubt he'll have that troubling side effect of having people's residual memories/personalities. Rogue's power sucking ability tends to be temporary, because, let's face it, if you have a single individual with all the abilities of the entire X-Men not to mention how many other people she has absorbed from, she's a walking talking Deus Ex Machina (not that Peter/Sylar aren't nowadays). But, let's say that Rogue would touch Storm and access her ability to control the weather (which she has done in the past). Storm passes out (usually this is a side affect of being absorbed by Rogue) and Rogue is flying around on wind and throwing lightning from her hands...then a few minutes later, Storm wakes up and the weather calms down and Rogue is back to her normal self.
Being Peter (and probably Sylar's) father, Arthur will likely be able to retain any abilities he's absorbed (and will be yet ANOTHER character with the healing ability), but once Peter is out of his general vicinity he should start to be able to feel his powers returning (as they did when he was captured by the Irish mob last year and as Sylar's did while he was travelling across Mexico with Maya and her brother).
I wouldn't be surprised, though, to discover that even if Peter is "powerless" he may have only lost his current catalog of abilities but probably retains his (and Sylar's) ability to absorb from those around him (his best bets in that room being Matt's father, since it's a hyper version of his own telepathy stolen from Matt as well as Knox's variation on super strength (since the rest of the villains are certainly afraid of Arthur). You just know that it's a matter of time for him to get everyone else's abilities back (at least from the main characters...Claire's, Hiro's, Nathan's, Angela's, probably Tracy's, Elle's, Daphne's, Meredith's (if he doesn't grab Flint's blue flames first), etc., though he can probably kiss Claude's invisibility goodbye).