Bad news mate. I watched it happen in real time.
Quick question first - are the new resources seed based or is there anything that could make them different on this update? My computer is too slow to load and unload mods and massive saves and wait for factorio to check consistency to answer my question, but I don't remember there being an ore deposit right below the core mining drill last time.
Anyway,
1) The core mining drill which was missing last time is now sitting on tantalite ore, and claiming "no minable resources"
2) The other core seam is sealed again. It is not directly adjacent to a still-existing cliff. BUT, it does have indite ore pasted partly over it.
I think that what's happening is like when you super force build a building over a core seam...
Funny coincidence it only happened on one planet, and right near each other.