From what I can see the only solution is to take the base apart piece by piece. This is going to be a massive pain in the ass. Is it possible to reset the entire home base so I can build it again from scratch. I have heard that destroying the base and collapsing stuff doesn't return the materials, so I can't do it this way. Surely there is a better way than taking everything apart piece by piece?
Sadly there is no way to reset your storm shield base. In fact, at the minute you can't even rename the thing. If you wan't to rebuild your storm shield base..well you cant. You need to destroy every piece of it and rebuild it from scratch. You wont get back any of the resources for destroying the base either. You will get to build other bases in the future missions though, so if you are on the first base and have realised that you have made a complete mess of the structure, just leave it. Learn from your lessons in the future and build a better base the second time around.