It is definitely possible to upgrade Moodle, with existing data. However, we don't have any tutorial on this activity in our series.
Pls refer to this webpage for details.
There is no problem with moodle upgradation.
Moodle Database and the files are separate. So, you will not run into trouble. Very rarely, you will be having to upgrade the database itself. We encountered it only once in a major upgrade. Other thing will all be fine.
Try to use GIT. I use git and it is as easy as git pull -a on an elevated command prompt.
install Git on your Ubuntu Server -> install git -> install apache, php, mysql(mariadb or postgres) -> create db users and passwords -> move to the webroot of server (/var/www/html/ typically for the Ubuntu environment.) use the instructions at https://docs.moodle.org/36/en/Git_for_Administrators
You are good to go.
Trust it helps.