When you (re)open a project in PHPStorm, it will ask you whether you want to open it in a new window or current. If you choose new window it will open another instance of PHPStorm and open there your project, if you choose otherwise it will replace the curent workspace with the new project. There is also a checkbox saying don't ask me again and then this will be the usual setting from now on. Now what if you did something and then you regret. It took me some time to find out how to change this. Here it is. It's quite simple actually and I would probably found it faster if I didn't google for it but just would use some common sense and find it myself (which I eventually had to reserve to since googling did not help)
It's basically Settings->General->Confirm window to open project in