Technically, they're "extinct"… as much as anything can be in a very big galaxy that has rubbish communication systems, semi-reliable FTL transport and vast sections that are otherwise unexplored or forgotten to the moldering passages of time and (heresy!) most of the Imperium is quite happy to bulls--t its population on a need to know basis.
As a GM, I'd have no worries about some of them at random waking up from the bottom of an oceanic abyss, unfrozen by miners who dig too deep on a distant moon and start running around wrecking all the imperial's junk. On a slightly more epic scale, they're fairly powerful warp-engineers and could just simply have retreated to a bastion deep in the warp itself, gearing up for 'Round 2' and bust out with an "Oh, you though you won?"