Z-wave has always been flaky for me as well. I stopped buying new units and went WiFi + 433 instead for my new house construction. Can’t keep adding on if the foundation is already creaking.
But, for removing old Z-wave nodes, I myself use the Z-Wave PC Controller software. Link in this old thread: [SOLVED] New UZB dongle, Z-Wave PC controller immediately exits (or crashes) with no error message - #11 by leif
This may or may not work with your dongle too. Probably will since all Z-wave chips are made by the same company.