What were the beings leaving the giant skeletons discovered in the late 1800s and early 1900s as reported in the August 17, 1885 New York Times?

These were indeed Anunnaki beings, so they are Anunnaki skeletons. And so this is the reason for their disappearance from museum collections. They have been gathered up and destroyed to prevent them from falling into human hands as an object of study, to open eyes, to even begin doing DNA studies on the remains which could catapult humanity forward greatly in understanding their limitations. So there is a high strategic importance to keep any Anunnaki remnants out of human hands and scrutiny.