Yesterday I tried to download all GTDB genomes with genome_updater, but only 402,538 out of 402,709 were downloaded. Because some of them are deleted in NCBI.
NCBI generally (never?) deletes data, but data records can become suppressed. For example,
GCA_024650005.1 has been suppressed, but you can still find information about this record and how to download the data at:
Thanks for the information.