Mail’s Vanishing Rules Actions
Each click on the Edit button eats a bit more of the space reserved for the Actions section. After about 25 clicks on Edit, the Actions section will be completely gone. (I have verified this on three machines, including a fully-stock El Capitan installation, so I don’t think it’s something on my end.)
At this point, the only fix is to quit and relaunch Mail—this will restore the Actions section, at least for another 25 clicks.
I’ve seen this, too.