You did not mention that before removing any disks you first need to copy any data you want to keep to another location as removing a disk from the array also removes any content it might have.
Once you have done that you can remove as many disks as you like in one operation as removing any disk invalidates parity so it will need rebuilding anyway whether you remove one disk or several disks at the same time. After doing the New Config you are free to change what slots disks are assigned to, and to remove drives you no longer want in the array When you start the array unRAID will recognise disks previously used by unRAID and their data will be left intact.