So during last week's session I rolled my navigator's warp encoutners and got the ghost in the warp outcome. Deciding to spice things up a bit I had the contact resolved by tthe ship's augers as their sister ship, lost some 600 years ago. My players however decided that was a prize worth risking it all and are looking at ways to board the ship and recover the vessel mid warp travel.

I'd like other GM's take on dieas and concepts for what they might find, complications that might ensue etc.

There's two branching possibilities I need to decide first

1) The contact isn't actually their sister ship, but a hulk of some kind the demons of the warp have conjured up to look like their desire.

2) The ship is what the sensors say it is, but there is a reason it was lost to the warp, great calamity has occured and the explorer's will need to fight survive before they even worry about salvaging the ship.

I would appreciate any ideas to mine from.

Offhand, I can't think of anyone even attempting (much less succeeding) in a mid-empyrean boarding action since the Inquisition War trilogy (either Inquisitor/Draco or Harlequin, although I think it was the former). In that case, it was in an area artificially cleared of minor warp entities (and possibly fused with real space- I'd have to dig it out and re-read it to be sure) by an unspecified means. Knowing the people behind it (or claiming to be), I suspect daemonic or xenotech intervention.

Of course, that was in a much earlier conception of fluff.
Assuming you want to go with an actual craft there (as opposed to a daemonically created phantasm to lure people out from their Geller Field), the big question has to be whether there's anything alive aboard the other vessel, and (linked question) is the Geller Field generator still functional? If there's no Geller Field on the other ship, then not only do your party's helmsmen have to maneuver their ship close enough that any boarding party can cross between the two vessels under the protection of their own home ship's Geller Field, but close enough to envelop the hulk (at least partially) and hold station once they manage it. And then the boarding party has to avoid straying too far and leaving the protected areas- and hope their ship doesn't put too much strain on the Geller Fields, or drift too far from the hulk...
If there is a working Geller Field, then there's less of a pressing need to hold their ship so close. Of course, that also means that there's a possibility of survivors aboard that haven't been made into daemon chow. Not necessarily sane survivors, or even human, mind you. Hell, there's plenty of room for massively and horribly mutated cannibal tribes as a result of warp exposure, or simply time spent drifting through the dark behind the stars, not to mention the possibility of a daemonling of some description sneaking in during a Geller Field flutter and finding itself trapped aboard.

The time to really worry (and torment them) is if there's no Geller Field... and there is something alive over there. It's possible, of course, that it simply lucked out and the myriad daemons and warp entities out there failed to notice them- but is anyone going to be that lucky for 600 years? Your options really are daemonhost(s), the horrendously mutated, warp resistant aliens, or possibly go with the Event Horizon scenario (the ship is alive now... and it wants to kill them).

I actually ran a similar thing as a small mini-endeavour. The group came across a vessel trapped in the warp. It wasn't daemon possessed or anything, they just had hit a bad, BAD spot of turbulence and were trapped in time. The group needed to make a highly modified exploration roll; the navigator makng navigation based tests to navigate through the turbulence without getting trapped, the explorator making rolls to reinforce and later merge the Gellar field, the Rogue Trader making command rolls to keep things tight. Once they'd got enough successes, they pulled alongside the vessel, convinced the captain that the Gothic War was over and that they weren't minion of the Archenemy attepting to persuade them not to invade/orbitally bombard a planet that had been returned to the Imperium centuries before, and eventually helped pull the ship out of the warp in one of the closest calls I think I've ever seen a Navigator mess up (so many fate points! Oh, the humanity!).

Took a full session, but the group eventually added the transport to their fleet while having a nice, tense time of things - no hellspawn required!

Or you could throw a spookier spanner about - the ship isn't really in the Warp at all, but is actually reflected from Realspace. The players can find out where in Realspace it is, but only by listening in to it's transmissions

The players ended up rescuing the ship, I went with the option of the ship being stuck inside a warp shoal or bubble. They had to get their own ship inside the bubble taking some damage in the process (and making some navigation rolls).

On arriving in system they were able to deduce that time passed slower there then in the surrounding warp so the ship had only been idle for a little over 200 years. They also started receiving the automated salvation beacon and deduced that no other coms were available on board the vessel.

When they took guncutters to board the ship they were fired on by the defensive turrets they took their point cutter and ran interference allowing the others to land. Their house troops established a beachhead on the vessel and rather spectacularly repulsed attempts to dislodge them by the mutant/chaos faction on board the vessel especially with the help from the navigators warp eye (turns out warp eye is shockingly effective against human/mutant wave attacks that arn't prepared for it.

They made contact with the other factions, got intel and used their ownss hips guns to blow up the derelicts fighter bays shreding most of the chaos aligned residents. Then they had to contend with the CoM First Mate who didn't much appreciate them trying to commandeer his vessel. They opted to have their NPC engiseer duel the opposing Magos, he "defeated him" and then claimed the vessel for the CoM and for their house. (It was originally a Disciples of Thule Vessel). They are actually a bit pissed at their Engiseer as he effectively made himself Captain of the vessel without consulting them. He for reasons of his own didn't see a problem with this, but now that their in such a snit about it is starting to question the wisdom of giving them his alliegance as they had already been treating him as a bit of a lackey. Now he is forcing them to treat him like a peer and they in turn are acting like he has betrayed them. I do love internal drama. Unfortunately for them since they know he is an Ordo Xenos agent in addition to the CoM they can't just space him for insubordination.