quick question about the flashbacks. In the OP it lists all the audio flashbacks, do these count towards the trophy? because during my big boss run, when I was in the blast furnace elevator, the audio flashback never triggered.
so Im wondering if they count audio flashbacks or only the ones that have an X and the two secret X pushers.
Supposedly the audio flashbacks do not count so if you miss them, don't worry about it. However, if you do everything else (beware of the briefings, it is very, very easy to miss flashbacks in them) and don't get the trophy, do them on your next playthrough but no, I don't think they should make you miss the trophy and I imagine that if you miss the trophy it is much more likely to be in the briefings than as a result of the audio flashbacks.
EDIT: Actually, Hydrargyrus, how much ammo do you actually have? On a Big Boss Extreme run you really do not need a huge amount because:
You should be avoiding enemies in most areas, only tranqing one or two in the way.
You should have at least fifty tranquiliser bullets starting the game (but if you bought the emotion ammo it shoots up to 250/300 I think so you should never even need more)
You don't need tranquiliser bullets in Act 4 (with the exception of the Beauty)
You don't use tranquilisers during the bike chase (which would otherwise be the most ammo-intensive area).
Most ammunition boxes are not too far out of the way of the quickest path through an area (a link to the list of where they are in each area is in the original post somewhere) which means you can collect one from whichever area you are in when you reach 10-25 tranquilisers without wasting too much time.
Honestly, the ammunition isn't too big of an issue and if you search enemies as Maddocks suggests it likely won't be an issue unless you tranquilise everybody (which will actually impede your progress as it will take too much time to do that).