Settings are reseted after Java update

[routeconverter]

Is that how it is supposed to be after Java update?

No, and I have no idea what happened on your machine.

And if so, where are those settings stored, so I could backup them in case of this happening again?

I've never heard of this before in 15 years. You can find the preferences in the registry below
HKEY_CURRENT_USER\Software\JavaSoft\Prefs\slash\