First of all NEVER “change” a source. You have pretty much two options that will not cause you duplicates in your library and dead links. One option is to delete your sources and select the option to remove the items from your library. You then setup a new library from scratch with new sources. If you don’t want to lose any tweaks and watched status you can export your library (to individual files) before removing your sources. You would then make an advanced settings.xml file adding in the option to import watched status. At this point when you scrape in your library new it will retain your old art and info. The other option which can be much less involved is to just configure a new location with the content using the same relative file paths (ie setup network file share and copy over the content from your existing hard drive exactly as is) and then use path substitution to tell Kodi to use the new location. With this method you make one file and change nothing at all inside Kodi. You just reboot and everything stay as it was with the only exception being your files are being pulled from the new location. A howto regarding this method can be found at the following…
EDIT: If you completely remove a library to start from scratch there will be a lot of old artwork and possibly some dead links left behind. It may be prudent to manually delete the Thumbnails folder along with texturecache13.db and if you really want to have a clean setup the video and music db’s as well.