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I'm trying to write a Dark Heresy campaign, but I wanted to keep it fairly in line with the 40k fluff...
Basically, a Sisters of Battle Cannoness (A particilarly renowned one) was captured by agents of chaos. (Khorne, probably.) They tried to convert her to chaos, but had no such luck.
However, her Armor and weapomd were left intact. A suit of Artificer Armor with an incorporated Rosarius, along with a pair of wired in Infernus pistold and with a built-in Jump Pack. Obviously, it is of extreme value and as such the forces of Chaos want to use them. Unfortunately for them, the Imperial and Adeptus Seals on it prevent any tainted or corrupted worker of Chaos from using it, and they are therefore stripping it of its wards one by one in an attempt to make the Asuit usable by an appropriate chaos soldier.
The inquisition doesn't know if she is still alive, but has dispatched a team to go on a search and rescue mission to retrieve her and, if possible, the suit of Armor as well. Does this seem plausible?

Sure.

Pentagrammatic Warding is detailed in.... I want to say Radical's Handbook, or maybe Disciples of the Dark Gods, but I'm not 100% on that. They have details of how such warded armor works, how the wards affect the Daemonic and the Corrupted, and how one goes about destroying them.

Yep - artificer power armour is often very valuable - certainly both sides would want to claim it, and it makes sense that there would be wards and whatnot on such a valuable item.

Depending on how callous your Inquisitor is, they might even value the suit more than the person wearing it, which could be an interesting dynamic - maybe the Inquisitor wants the suit for themselves?

And of course, no-one in the Inquisition would want to have a chaos champion running around in a suit of artificer armour. It's bad for business

So the reclaim team makes perfect sense as well, and the wards are established too.
Sounds good.

The suit is the priority, especially since there is a chance the saint is dead. I'm not going to have any specific rules for how the runes work beyond maybe +1 or 2 Armor against daemon or chaos-based attacks, assuming that the players take it for themselves.

One thing you want to consider is the nature of your Inquisitor should the suit be found... "modified". Or even stripped. If they're a puritan, they'll want to destroy it due to the taint. A heretical erm, "unorthodox" Inquisitor might well end up using it themselves or giving it to a bodyguard if they're the wrong gender.

Waaaghpower wrote:
The suit is the priority, especially since there is a chance the saint is dead. I'm not going to have any specific rules for how the runes work beyond maybe +1 or 2 Armor against daemon or chaos-based attacks, assuming that the players take it for themselves.

There are specific rules for runed/warded/holy armor in the various DH books. Most common is that they provide the armor's standard AP against Daemonic/Psychic attacks that normally ignore Armor.

Waaaghpower wrote:The suit is the priority

I'd say this depends on three factors:
- how old the suit is and who wore it before, i.e. if it qualifies as a true relic by itself
- how renowned its current owner exactly is, both in terms of public as well as political influence (which is usually connected, but there are exceptions)
- who actually ordered the rescue mission

Normally, it is the Sisterhood who would be expected to despatch a mission to save their heroine (or recover her remains for proper burial), but it is entirely possible that the Inquisition gets involved as well - either because a Puritan Inquisitor feels it is warranted, because a neutral Inquisitor wants to collect or repay a favour with the Sororitas, or because a Radical Inquisitor would like their hands on that suit of armour. It is entirely possible that both the Inquisition as well as the Sororitas conduct their operation independently from one another (with potential for a violent confrontation if they meet unscheduled), or that the Sisterhood is entirely unaware of the matter and thus left out.

If the lost suit of armour is not itself a relic, the Sororitas (as well as many Puritan Inquisitors) would very likely prioritise its owner, for Imperial heroes are generally held in higher regard than technology by them, and the Sisters would gladly trade a hundred suits of power armour (and their wearers, if need be) for the left thigh bone of some long-deceased saint. This is different to how both the Imperial Guard as well as the Space Marines treat the value of machines - the former because a Guardsman is worth gak, and the latter because they really revere their equipment a lot once it has achieved a certain age.
Of course, if the suit itself was a relic, things are different for the SoB as well, and studio fluff notes how many Ministorum priests cringe at the Battle Sisters carrying important holy relics into battle time and time again rather than locking them away in some vault to collect dust, so this is also a possible angle.

The above is my opinion based on GW fluff, but I'd say you have a lot of options for paths to develop your story to.