Just run the install script to update.
The database is always left alone, no matter if you run the install or uninstall script.
(the uninstall is mainly so it stops CPU by creating graphs and will also stop data collection which incurs some writes)
I’m not really concerned with the few MB the database occuppies.
Deleting the database would also be really bad form.
There is no way to know the version you are running 
In doubt just update by running the install script, it doesn’t hurt anything.
I’ve even made a script to convert the database to the current format.
But you only need to do that if you are limited to one year and want 3 years of history.
That’s only the case for people with a database dating back to the adsb receiver project from which i forked my graphs.
I made some minor changes to the database format, but rather soon after releasing the initial version.
Install/update:
sudo bash -c "$(wget -q -O - https://raw.githubusercontent.com/wiedehopf/graphs1090/master/install.sh)"
!!! the following is not necessary for most people !!!
Update database format (might screw with the max range graph a little, don’t interrupt it)
(also: run the install/update first)
sudo apt update
sudo apt install -y screen
sudo screen bash -c "$(wget -q -O - https://raw.githubusercontent.com/wiedehopf/graphs1090/master/new-format.sh)"
Also this takes around 8 minutes, no data is collected during that time period.
(edit: added protection against ssh connection loss, so the process will still complete)
As i said before, this isn’t strictly necessary.
It’s been quite some time since i settled on this iteration of the database format.