If it helps, try buying a portable map, then look on your base's map for different ping signatures. If they are still around, they should be one of the pings. Just follow the coordinates and seek it out. I had to do that once when mine disappeared suddenly in the last update. Thought he was gone and eventually had to find them through coordinates.
Viewing post in Kerfur omega flesh pit + disappearance
Have you checked each ping personally? I know it may sound redundant, but I did see someone suggest to check out your windows, so checking the pings close to your base might be worth looking into, as well. Especially when things on the map appear close to your base, it's hard to determine what's new, what was there, and what wasn't.