Where you setup your sources you can context menu and tell it to delete a source. When you do that Kodi asks you if you want it to remove the items from that source from your library. Additionally/alternatively your existing library sources are tied to a external drive so you could not have that drive plugged in and then run a clean library which would then tell you that your source is missing and ask you if you really want to remove those items. If you tell it yes then it will remove all the items from your library that were pointing to that drive that is not currently plugged in.
Assuming you didnāt manually configure anything for your external drive mount it would have automatically be setup as a mount in /media/[drive name or UUID]. In a network setup you would either use Kodi paths (Kodi directly handles the connection so there is no system mount) or else manually configure a mount probably via autofs but the norm would be to do this at /mnt/[something] so this wouldnāt be such a issue.
Iād suggest since this is new to you that perhaps you donāt start out by trying to switch your library over but rather just keep doing what your doing now and play with a network setup with just configuring a source but NOT configuring a scraper so it doesnāt interact with your library to start. You can manually just browse the files in the network location via videos>files or music>files. In this way you can make sure you have everything worked out without having any kind of pressure or down time.