Hi,
Hazel is randomly deleting rules and folders (in the preference pane, not the folders themselves) to which rules are assigned. It's occurred with 3.x versions on an ongoing (seemingly random) occaisional basis, and has done it twice in the past 24 hrs on version 4.0.1. - once during the day while using the machine, and once this evening while the machine was idle.
I thought it was something I might have done in the past, but today made it clear that it didn't require any input or action on my part.
I'm running 10.11.4.
Hope you have a "fix. I love Hazel but this is really irritating when you count on the app.
Thanks!