A little bit of background real quick, my group is running through LotE and just went through the Zayth portion and faced down the Gun-masters and their minions. My guys have a fairly high PF and everyone is in Power armor of some form or fashion, so I ended up putting them up against 15 gun master and 60 of the minions and ran it like you would a Deathwatch scenario with the minions being split into hordes. Due to the power armor, two of my guys were nearly invincible, with only head shots being able to really injure them, and one of the (the navigator) ending up at 0 wounds from 1 round of heavy stubber fire. They cleaned up fairly nicely, a few wounds being handed out due to headshot rolls, but for the most part came out ahead of the curve for the bodies they left behind. Our RT (who has Unnat Toughness) was even the epicenter for a Melta Grenade launched by the Magos present, and didn't take any wounds (due to a low damage roll).
I was slightly dismayed after the combat, as I'm having a bit of difficulty threatening our two tank character without using anti-tank weaponry, so I've come up with a scheme to maybe get them out of the powerarmour and into some slightly less strong armour types.
I'm going to introduce upkeep tests after combat when the characters have taken hits that have penetrated their armour values. During combat, they have what the stats say, but after the end, their stuff might be in poor shape and need repairs, hence the roll. I could even increase the negative to the roll based off the number of hits, thereby making heavy stubbers an annoyance at least.
I don't think they'll object too much, but I wouldn't mind some extra feedback before I introduce it.