Hi Stephanie,
I’m not entirely following the issue here. GTDB-Tk does not change the names of input genomes or attempt to map them to the GTDB. All your query genomes passing QC should end up in the output with a name derived from the input filename (or the explicit name you gave them if using a batchfile). Perhaps you can send me an image and small dataset that illustrates the issue.
Cheers,
Donovan