by chance do you know what exactly does "fleet prepare db" if the database is already initialized and with data from a previous version of kolide?

It performs the SQL migrations. If there are no migrations to run, it does nothing. We use

fleet prepare db

as the

ExecStartPre

in our systemd service file

so it's safe to run, no data wiping right? i asked because i think that's the same command we issued to initalized the DB

No data wiping. It runs the SQL statements contained here: https://github.com/kolide/fleet/tree/master/server/datastore/mysql/migrations

Fleet migrations are designed to maintain your data. That said we absolutely recommend performing backups before running migrations. Basically agreeing with everything @sundsta said.