@naushadnaleer We don’t have updated recommendations for migrating from Archiva to Nexus Repository 3, we don’t hear about Archiva very much any more!
As you say, the on-disk format is different, so the approach that worked with Repo 2 won’t work. You can either follow the Archiva-to-Repo-2 instructions then migrate from 2 to 3, but if you have a relatively simple setup you might instead look at using the Repository 3 Pro Import functionality. If Repo 2 could ingest Archiva’s on-disk format, then the import may well be able to as well.