Kevin,

I'll take a stab at it . In advance, forgive me if I'm about to tell you things you already know.
Many of the caves in the Hill Country around the Austin area contained huge colonies of bats ( as they still do) . The caves are full of bat droppings or guano which have a heavy, sharp , "ammonia-like" odor . The guano is a rich source of "nitre" or niter , which is also known as saltpeter( potassium nitrate ), which is ( was ) a key component in the manufacturing of the type of gunpowder that was used during the WBTS. "CSA Texas" actually shipped a fair amount of the stuff ( nitre) to the big CSA Powder Works in Augusta , GA as long as they could get it across the Mississippi River. After the fall of Vicksburg , the "Texas nitre" had to be used closer to home in places like Tyler , Spring Creek ( near Tomball, Tx) and other sites I am unfamiliar with but others may know about.

As far as the troops who guarded these caves or guano deposits, I really can't give you a unit name or regiment; however, my guess is that state troops , local militia , reserve troops or even military cadets from Austin or Bastrop would have been used for this duty. The main threat at that time in the Hill Country area northwest of Austin would have been from Indians such as the " Lords of the Plains" (Comanches) , who were taking full advantage of the absence of Federal Troops from the "frontier" . Now I don't believe for a minute that the Comanches were into making gunpowder in the 1860s and I don't think they had developed a taste for bat meat ; however, If there military troops around , that meant that weapons, horses, cattle, mules , other food , clothing, ammunition and valuable captives ( especially women and small children ) couldn't be far behind. The Texas Rangers ( not Terry's 8th Texas Cavalry) did the best they could to keep the Indians at bay, but there was just too much territory to cover effectively . I also don't believe that the fairly or unfairly maligned Captain/Major/Colonel James Duff of "Massacre on the Nueces " fame (infamy), and the "choir boys" of his Partisan Rangers would have been satisfied with guard duty at a "bat cave" either. I think that also applies to "Rip" Ford and his mounted outfit as well as that of Santos Benavides of the 33rd Texas Cavalry ( an unsung hero in my book) .
I apologize for the long comment. I don't know who was stationed at the cavern ; but I'd doubt that it was active, "front line" mounted units . Those troops were either along the coast , along the Rio Grande border , up in north Texas along the Red River , or helping out in Louisiana or far east Texas.
Good Hunting , Craig