Minimally-useful me-too anecdote: I've also had mining depots & associated mining drones disappear.
I initially assumed user error, but it's happened enough times now that I suspect something more systemic.
Haven't been able to reliably reproduce the issue. I'm not using ATO, but I am playing a heavily modded setup (K2, BZ, etc.).
FWIW, the two ores I can remember being affected:
- Nickel (https://mods.factorio.com/mod/IfNickel)
- Wolframite (https://mods.factorio.com/mod/bztungsten)