After the most recent update 2.9.24, when I select several messages in the Spam folder as Good in Apple Mail, it clears out the whole folder and moves it to the In Box. I then have to go to the In Box and mark the Spam. Also, the colors in the Spam box no longer appear.
I’ve never heard of that happening before. Does this happen every time? Do you have more than one window open in Mail? Please describe exactly how you are marking the messages as good.
Are you referring to the message background colors (the normal SpamSieve behavior) or the colored flags (enabled by an optional rule—you had tagged this post “Colored Flags”)?
Also, please check whether you have other Mail plug-ins installed.