Thanks for your kind words and for sharing! It's really nice to hear that Hive Time has whet your appetite for management sims :)
You will lose some of the resources spent on constructing the cells you're destroying (by default, destruction gives back half of the current construction cost). If you have enough redundant storage cells to hold your entire current stock of a resource, you won't lose any of that stored resource when destroying its storage cells.
My intention is that this promotes hive expansion, leading players to build bigger on their early hives rather than reconfiguring a limited space while they're still learning. Ideally, this pushes the challenge of chasing highly optimised spaces for players' subsequent hives, where the fiddliness of destruction and potential loss of resources help provide some constraints that make that kind of gameplay a tiny bit more technical.
If you do decide you want to start a new hive, the game will automatically make a save of your previous hive just before you left so that you can go back and load it up if you change your mind. There are a couple of things that won't happen on your first hive, but playing a single hive forever is a valid way to play ^_^