Hallo there,
I’m in dire need of some advice on a Warp-capable transport ship.

1) Point of the story and planned development
At the end of the current adventure, my group’s Inquisitor will be sending the PCs to a paradise world on a one-month prize holiday, as he already did some times before.
This time though something will happen during the travel: a Warp storm will change the ship’s course and let her out at the opposite corner of the galaxy, on the fringes of the Tau empire, more exactly close to a human-inhabited, blueskins-owned planet.
The outline here is to have the PCs to be well received by the human hippie commies and forcibly incorporated into their community: my players will have to figure out a way to escape from here.
After this, the long journey home begins, divided into a myriad of mini adventures, the first of whom being the PCs getting into an Imperial fleet and, should they claim being agents of the Inquisition, being handed over to their Inquisitor’s rival Inquistor (I don’t think I will develop the puritan/radical rivalry though since I didn’t incorporate it nor hint at that in any of their previous adventures).

2) The ship they’re currently using
To bring them into this adventure I thought to have my players fly the same archotech shuttle their Inquisitor loaned them for their previous travels to the same paradise world: it is Warp-capable and fast even though it’s manned by a pilot only (whom they made friends with).
The escape plan from the Tau planet I sketched out provided that my players had to rescue both the pilot and the shuttle: of course, should they come up with different ideas, I’d been glad to indulge their plans but still I needed one, in case they didn’tcome up with any.

3) Where the current ship doesn’t fit
The shuttle though - ad its pilot - are an hindrance for the plot’s continuation: after their escape from the planet, I need the PCs to be kind of stranded, with no other means than their wits and what they’re wearing, and have them get their equipment anew, as their journey home moves forth.
They would also be unable to use any Warp-drive on their own but rather forced to scrounge, buy or earn a lift on liners.

4) Where I need help
Since the Inquisitor’s shuttle is too valuable to be lost and I don’t wish the pilot to be killed (he’s grown into a reliable and successfully portrayed NPC), I’m uncertain how to link the PCs travel to and from the Tau planet with the first of the following series of microadventures.
So I really need a suitable transport to the paradise world and thus to the Tau planet : it should be carrying very few people (even better if it’s the party only), expendable and likely usable as an escape ship.
I’d wish to avoid the «huge ship crushing whose only survivors are the PCs» stereotype because I as first wouldn’t be at ease with it.
Any idea?

5) The PCs
Currently the party is made of a guardsman, a scum and a void-born adept with some skills at piloting and navigation (she could be driving the escape ship).

Thank you for any assistance you’ll give me!

I can't help you with a ship. But you could use a regular void ship with thousands of crew and after the crash have the surviving crewmembers prefer to stay on the hippie-planet. Life there likely beats life aboard a void-vessel....And that would provide adventure hooks as these happily stranded spacers don't want the Imperium to find them and will try to prevent anyone escaping the woodstock planet and rat them out.

Another option is to still go with your super-small warp capable shuttle. As it has only a pilot, the vessel lacks a navigator and thus can only make short jumps along well known shipping lines. Finding himself at the other end of the galaxy means the ship is useless without new (reliable) charts. So your players would either have to get their hands on such charts (good luck with that as they are virtually priceless) or get aboard a ship which can travel this part of the galaxy. Or it would take forever to make short jumps without a navigator...Take your pick.

Alternatively, you can easily rule the warp engines have been damaged by the crash or the violent warp storm. Especially in such a small vessel, there won't be any redundancy in-built or back up engines. And on the hippie planet, there are no parts available to repair the engine (even if your players or the pilot could but that seems unlikely with the mechanicus monopolizing tech use and the semi-religious nature of tech. Not like hitting it with a spanner and yelling at your hairy sidekick...Now the shuttle only has its plasma drives left enabling in-system travel only.

Hope this helps...

Would it be possible for the Players to stumble across a Space Hulk? Like Judgment Of Carrion ( http://zen-master.deviantart.com/art/Space-Hulk-163631830 )or something similar?

There could be a distress call or something of the sort that lures the Players or the Pilot to board the Hulk. Once on board the Players could find signs of a battle struggle. Heck you could foreshadow what's about to happen next with Tau weaponry found on the "ship". While the Players are investigating the ship starts to go back into warp and are trapped from making back to the shuttle.

The space hulk arrives back to where it originated deep in Tau space near the "Imperial" colony.

The colony could be the original survivors from those that abandoned ship back when it was still a ship intruding into Tau space. The only way off the ship would be an escape pod or if the Players manage to send out a signal that attracts the Tau or Cutter from the colonized planet.

Once on the planet things will seem odd, specially if there are Tau there too...

Investigating the Players could learn about a handful of survivors that left to return to the Imperium. Maybe the Captain's data log (conviently left behind) stating that a handful of survivors are not content to be here with the Blue Skins, plan to make back on board the ship/steal a cutter and find their way back to the Imperium. using the notes left behind or navigation charts on board the space hulk to find a way back...

Just a thought...

I like the idea- a venus-fly trap ghost ship that captures those that have been sent to investigate it and, due to some pre-programmed machine spirit protocols and routines, warps the entire lot back to the plant where it started its trip.

You can start off the mission as an event Horizon type horror game before they take a shuttle and escape, blowing up the ship and ending the cycle.

Thank you very much for your advice: I like both the hints about the shuttle’s spare parts/charts and the space hulk coming back or linking back to the Tau space.
I think you put me on the right path: now I only have to process these ideas and put them into the adventure.

Sorry if I didn’t reply sooner, when I posted my question I didn’t consider I hadn’t been able to access the Internet for some days until today.