You can regenerate your universe in Portal Knights at any point if you want to reset it. Doing this will remove any change you have done to any island, reset all quests, and reset all resources that are found on the islands. That means that you can loot everything again, and mine islands that have already been mined extensively.
So there are both benefits and negative consequences to regenerating your universe, but it's actually very easy to do. In order to regenerate it, go to the main universe selection screen, press the Settings option there, and click on Save Data Details. This screen allows you to chose the Regenerate option, which will first present you with a warning (that you should read), and of course allow you to regenerate your world.
The only things you will not lose by regenerating your universe are things and changes to your "Home Island", and the unlocked portals. So make sure to store all your valuable items on your Home Island before regenerating your universe.