Well, this question is about Overpass API, so there aren’t any planet_osm tables whatsover.

Those are warnings which occur during the import process. They shouldn’t abort the import itself.

Running Overpass API on an extract is challenging, using multiple extracts will probably expose other (new) issues, unless you manage to merge different extracts outside of Overpass, and provide proper .osc files. Major issue here is, that this setup is untested and unsupported!

Why don’t you go for a full planet instead and save you lots of effort to get this going?
Without attic data that somewhere in the 150GB range (including attic: 240GB).