Yes, if you delete a network the configuration will be lost.
If the network that your switches are in is a combined network then you need to split the combined network so that you can then combine the Switch network with your other Appliance and Wireless networks. When you split a combined network you potentially get multiple networks. E.g. if your network is called 'Site A Switch' you'll potentially get 'Site A Switch - appliance', 'Site A Switch - switch', and 'Site A Switch - wireless' networks. If you only had switches in that network then the two new networks, 'Site A Switch - appliance' and 'Site A Switch - wireless', should be empty and can safely be deleted.
You'll then have the appliance network and wireless network that you originally had, plus the new 'Site A Switch - switch' network that was created from splitting the combined network. At this point you can combine those networks into a single network.
So even though the network that contains only the MS devices is a combined type, I'll have to split that and I'll get three networks such as an appliance type, wireless type, and whatever other type category there is. So the resulting networks I'll get from splitting this combined type network would give me an empty appliance type and wireless type.
Just making sure I understand correctly.
Will I lose any configurations on the switches from the combined network that I split?