I’ve been complaining about this for years. They fixed it. The NCBI have reorganised their genomes FTP site and finally, Archaea are not lumped in with Bacteria.
GenBank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/ RefSeq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/
Archaea are still included in the ASSEMBLY_BACTERIA directory; hopefully that’s next on the list.
[*] to be fair, they’ve always recognised Archaea – just not in a form that makes downloads convenient