When CommandBox updates the libs, it overwrites the web and server context config XML files. This can be tested like so:
It has come to my attention that this removes vital information about installed extensions, which Lucee does not automatically replace on the next run which can affect the extension management funcions in Lucee as well as cause OSGI bundle errors on startup.
You can see debug output that shows the skipped files like so:
Also, stop blowing away the bundles folder for Lucee as it is removing bundles that extensions were dependant on to work. I THINK not removing the lucee-server.xml file will actually fix the root issue that the deletion of the bundles folder was trying to solve in the first place.