I
believe Netbeans doesn't normally create any hidden files. So unless you've created them yourself, or you're using a plug-in or other tool which would create them, you don't need to worry about hidden files. To make sure, just try to search for hidden files in your original project folder - if there aren't any, you're safe. (If there are hidden files, you need to find you why they are there; only then can you decide what to do about them in the new project.)
As far as version control goes: if you aren't using one, this doesn't apply to you. If you're using one, hopefully you know how to add a new project there. By the way, this is the right forum to ask questions about version control too!