You can delete the entire /Backups directory—it’s your server—but doing so will nuke all backups, including the one 45GB backup you said you need. If you’re fine with losing everything in there, here’s how:
rm -rf /home/amp/.ampdata/instances/Minecraft01/Backups
Warning: This will delete everything in the directory with no take-backs. If that’s cool with you, go ahead.
If you only want to keep the 45GB backup, you should have tried identifying which file it is first, but since your listings seem broken, this could mean even the backup metadata isn’t working right. Up to you, just double-check before pressing the red button!