So, the ship has only 1 Navigator, and they are in a 15 days trip through the expanse...

What happens when the Navigator needs to take a leak? Or sleep?

Does the ship stop? Is it able to navigate for some hours even without a Nav? Does the ship translate into the void an wait for him to rest?

If you have 2 Navigators, can you run indefinetely without having to drop back to real space at some time? Can it reduce the time of passage?

Navis Primer , Pg. 29

THE NAVIGATOR’S SOLITUDE
As soon as the captain gives the command for translation, the Navigator must be left alone (aside from the company of his kin), for he must open his third eye when navigating the Warp, and the baleful, green energy that washes from his forehead can kill a normal man. Any non-Navigator within 15 metres of a Navigator engaged with steering a vessel through the Warp counts as suffering the effects of his Lidless Stare power (see page 180 of the ROGUE TRADER Core Rulebook) each Strategic Round.

THE NAVIGATION STATION
A navigation station is a highly sophisticated and little understood console of ancient tech. By plugging himself into this arcane throne via cybernetic implants in his skull or spine, a Navigator can meld his mind with the ship’s machine-spirit. This allows him to interface his psychic penetration of the Warp with the cogitators on the bridge, so that his mental commands can be translated into signals that the officers on the bridge can recognise.
If a ship’s navigation station is damaged, a Navigator must communicate his orders to the helm verbally, which is difficult for him to do coherently when he is in the trance state required to penetrate the Warp, and he suffers a –20 penalty to his Navigation (Warp) Tests. If a ship does not possess a navigation station for any reason, he suffers a –40 penalty to these Tests.

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From my understanding, the Navigator is basically put on life support while in a trance-like state, using his warp-eye to see the warp. All his physical needs are taken care of while he's navigating.

If the facilities for this process are missing or damaged (say the navigator has to use the toilet, or gets tired) I would use the penalties listed above since Navigation (Warp) is an extended action.

Keep in mind also that most Houses will also send several apprentice Navigators along with the PC, both to learn from him during his travels, and attend to his physical needs. Only a poor House or a desperate captain would have a single Navigator aboard.

Yeah, ships often have redundant "this station" crew, except for the RT, themselves (and I suppose even that MIGHT be possible, say if two kids are "competing" over Mommy or Daddy's Warrant rights), so they should have a cadre of Navigators, Astropaths (choir(s) and all), etc.

As for swapping out, I would imagine that the Navigator can't just step out, and let someone else take over; Navigators each see the Warp a bit differently, as their gene masks the Empryean in something they can look at, and not go nuts (even Navs don't truly look into the Warp as it is). So, they would have to stop, and do all of the "regular" stuff their colleague did, to see where they are, where they are going, how the Emperor is doing compared to the scenery that blocks him, and such. Since there are tales of ships trapped in the warp, I would assume that the ship doesn't HAVE to translate back to realspace for the stuff.

Also, I can imagine a Navigator wearing a suit that collects waste, sort of like an astronaut here might. Otherwise, the trance should allow them to hold it, and they could do an Austin Powers after the trip. I know in my story, the Navigator does her thing, and the immediate follow-up to realspace re-entry is stumble to her lover's quarters, if he's not waiting in hers, and CRASH.

Does Lidless Stare affect you if you can't see it? In said story, Arin fights his way into the Nav Chamber when some stuff goes bad, and he wears a blast shield helmet to cover his vision against looking out the window, at the exposed warp, using his other honed senses to find Asteira. She has Lidless Stare +10, so when he rushes up to her, and tries to bring her back to her senses, to drop the ship back to realspace, is her power going to floor him, or will the helmet, which completely blocks his vision (think Luke Skywalker's training scene helmet, used to avoid bright blasts in space) shield him?

Rules-wise, I can't remember.

Background wise, certainly. There are several examples of blind people being able to safely interact with navigators, from the marine engraving a navigator's eye by remote in the Inquisition War trilogy way back when all the way through to the blind servants attending the Excoriators Strike Cruiser navigator in Legion Of The Damned.

Think of the mind-strain it would be for a navigator to stay 1 entire week inside the warp illusion. I still think a part of the reason for the periodical stops is for the actual rest of the nav.