I also suggest you to talk to your DM. But with different approach.
Playing really big dungeon in 3.5e rule is often cause trouble, as 3.5e is assuming that PCs will sell/buy/create items (both magical ones and mundane ones) regularly. The game is balanced as such.
So, not just for your acid flasks, but for all the PC's equipment, some solution should be needed IMHO.
In my play group, it is usually done by intensive use of Planar Ally spells. If your party is L12 and have a cleric, favored soul or similar divine caster, the spell should be available. We often use those spells to, say, call a Mercane or Jinni, and ask for trade. If the first one come was not a trader, then we ask the name of easily accessible and trustworthy planer trader. Then, call that trader whenever possible.
By calling the same outsider again and again, you can even "order" a specific magic items which suit to a members of your party ("Hey, Granduaran the Mercane, please bring 20 flasks of Holy Water and +2 adamantine greatsword for trade next time", etc.) . 500XP per trade may seem a big risk. But usually, it ends up beneficial enough. And IMHO this is rather nice way to use this spell. Not broken, and useful enough.