Figured it out. While dealing with other pI3 issues I deleted these libraries OUTSIDE of pI3. That was the mistake. Therefore the "delete library path" button did not show up in the library manager and I was stuck. My solution was to re-add the library paths - each with a copied emitter in them - outside of pI3. Then in the library manager the "delete library path" button appeared and I could delete those paths. I then deleted the folders form my hard drive.
In theory there's no difference between theory and practice - but in practice there is.