Collections fail on restart

Every time I restart my lucee/tomcat service it fails to read collections correctly.

Environment: Ubuntu 16 and Windows 10

On restart of services, hitting a page with the the search page first returns “cannot create search.xml, already exists”. And every subsequent request sees a “collection not found”. Trying to create a collection ends with a “java.lang.NullPointerException”. The only solution I have so far that works is to stop the lucee service, delete the WEB-INF folder and totally recreate the DB sources and collections. This… is not ideal.