Hi,
You can update you new SSH Key on your probe's page such as https://atlas.ripe.net/probes/1000000/ on the bottom you see "Update SSH Key"
Otherwise you can backup your two key files [/var/atlas-probe/etc/probe_key and /var/atlas-probe/etc/probe_key.pub] before any update/reinstallation, and overwrite them back after new installation and reboot.
#!/bin/sh
systemctl stop atlas
systemctl disable atlas
systemctl stop var-atlasdata.mount
systemctl disable var-atlasdata.mount
rmdir /var/atlasdata
rm -r /var/atlas-probe/.ssh
rm -r /var/atlas-probe/bin
rm -r /var/atlas-probe/crons
rm -r /var/atlas-probe/etc
rm -r /var/atlas-probe/run
rm -r /var/atlas-probe/state
rm -r /var/atlas-probe/status