For some reason the Set/Clear Flag keyboard shortcut (Shift-Command-L) is not working. It looks like it’s been removed entirely. I don’t see the shortcut listed under the Edit menu. (I see the option to Set/Clear Flag, but not the keyboard shortcut beside it.)
I’m not sure how I removed it. How can I restore it?
Curious! You might check in your systemwide keyboard shortcut preferences. macOS has the ability to define custom shortcuts per application – it could be that an override there is interfering with the default Flag shortcut.
This Apple support article describes the process of setting a custom keyboard shortcut on El Capitan. (I believe the process is substantially the same for Sierra.) If nothing there looks amiss, you might get in touch with our support team – they’ll be able to dig into this issue with you!