Nah, you way off on that, coastlines have remained relatively same last million years, def not subducted into an ocean trench
We have plenty of fossil evidence from, from your example, a million year old hominids. Far more than we would need to expect to see evidence of civilization.
Subduction makes up for a tiny tiny proportion of where coastal land "goes" in any age.
You'd need an enormous set of coincidences for a past civilization of hominids to go unnoticed.