After cloning a drive and booting from it, Little Snitch asks whether to use the default rules or "this version" (meaning the configuration file that has been changed "behind it's back"). However, perhaps since LS 4.0.4 (but I'm not sure when it started, although definitely only recently), even when selecting the "this version" button, LS only has the default rules in effect!
The button to enable the replaced configuration file had been working fine for years, but now seems broken. I have not tried to use the "default rules" button to see if somehow they have been swapped. Of course, there is an easy work around that works fine for me: just import the rules from the global configuration file on the original drive. But this should not be necessary, right?
And thank you Objective Development for a wonderful product.