"Do you use any equipment for subsurface mapping; magnetometers, ground penetrating radar, etc.? How would one go about preserving a site that is buried and uncharacterized?"
I've basically worked for archaeologists. On a few sites, for the EPA, or over thought Watervliet Shaker burials, in that case the GPR was backed up by 3 backhoes digging 10 days for Dayton Power and Light in Ohio, just in case the historians were right! I've used some magnetometer surveys for others, one in the historic West Point Foundry marsh periphery, where I found out later, the leftovers from 1 million artillery shells from the Civil War might still be around. Wish I had known before! We did find the prototype of the "Swamp Angel" platform used in the 1863 bombardment of Charleston South Carolina, the Parrott gun that exploded is said today to be in New Jersey in a park.
I guess if enough documentation and certainty of a site buried and uncharacterized could be preserved from logical argument. If the argument for the enlisted mens latrine were found outside Fort McHenry in Baltimore, for example on a map or in a journal, it might be set aside from development, the kidney shaped brick thought "two holer" next to the bombproof inside the fort for the officers had been documented, circa 1978 though I now wonder having dug in it then, if it's not a latrine at all, there is another deep stone pit next to the bombproof site at Fort Montgomery, NY above the Hudson River recently opened, maybe for "bomb disposal". A major battle was recreated there for its opening.
I read a lot of urine was collected in the South during the civil war for gunpowder production. That kind of collection site might be "discovered" and preserved through the logic of documents presented. But maybe that's just obvious, from my view documents might be enough, artifacts could be mis-collected too, i.e., from the inside of a foundation, instead of artifacts from the "builders trench" left in the building of the foundation.
I once dug in a front yard for the site of the old redware Greenport Pottery for another archaeologist and a historian from American Studies in Cooperstown, NY. That's thought under present houses on fill that an underwater archaeologist is investigating collecting ceramic sherds from the underwater surface next to the shore, the "factory" survives only in a painting out on the east end of Long Island, NY. It's where many, even back when George Washington was off to Boston after the French and Indian War on a doctor's recommendation, traveled to catch a ship to Boston, bypassing the many rivers to cross in Connecticut. GW was at a widows place for three days a marker states. A railroad ran to it from New York City bypassing all the towns until it became the Long Island Railroad, after the bridges were built in Connecticut.