Kodi only cares about the file path, so if you maintain that then there wouldn’t be an issue. I’m not sure why you would need to mess around with a nomedia file though. If you format a new drive as ext4 it is going to mount as /media/[something] and Kodi isn’t going to do anything with that file path unless you tell it to. So you can just keep using Kodi as you normally would while transferring files from an old drive to the new. As long as the directory layout remains the same then once the transfer is done you can just remove the old drive, relabel the new drive to match the old, unmount remount, and Kodi is none the wiser. There is no need to do anything more involved.
If your current drives are smaller in size and you wanted to consolidate them to a new big drive then you could transfer the contents of each of the old drives to their own subfolder (ie /media/newdrive/olddrive1/) and then use path substitution to maintain your current Kodi setup without having to reconfigure and rescrape.