A list of the names of all seven Vortigaunt Xen maps, courtesy of CUE:
1 bm_c4a3a The Vortigaunt Village (bit 0)
(the map after that one, bm_c4a3a1 Gargantua's Lair, has no vortigaunts)
2 bm_c4a3b The Cable Puzzles, MISS (bit 1)
3 bm_c4a3b1 The Controller Fights, MISS (bit 2)
4 bm_c4a3b2 Gluon Gun Upgrade, MISS (bit 3)
5 bm_c4a3c The Conveyor Belts of Hell (bit 4)
6 bm_c4a3c1 The Attack of the Controllers (bit 5)
7 bm_c4a3c2 Shielded Controllers Introduction (bit 6)
You don't have to avoid killing all the Vortigaunts in all seven maps in a single playthrough. If you messed a few up, you can load the maps you missed afterwards individually by executing the console command "map [mapname]", then go through each again from start to finish without killing any vorts.
To figure out which maps you've already pacified and which you still need to pacifist run, open your achievement progress file (whose default location is at C:\Program Files (x86)\Steam\steamapps\common\Black Mesa\bms\gamestate.txt ) in a text editor. Scroll down to the data value of "27", which should be on line 191, containing a value that looks like "0x00000000000000##". Copy those last two digits and paste them into a hexadecimal to binary converter. The result should be a seven-digit number made of 1s and 0s. The 1s represent maps you have pacifist ran, and the 0s represent the ones you haven't. As far as I can tell, it's also in reverse order; the leftmost digit is what CUE calls "bit 6" and the rightmost "bit 0".