The issue with unavailable devices after 2nd reboot has been reproduced and it seems to be related when upgrading from 6.41.4 (or older) RouterOS/RouterBOOT versions. Our apologies for the caused issues, the fix will be included in upcoming releases.
So anyone using older than 6.42 RouterOS or RouterBOOT versions, please first upgrade RouterOS and RouterBOOT to 6.48.4 or 6.47.10, and only then use the latest version.