A self-update could relaunch Skim into a window with a titlebar and nothing. Restarts didn't help. Reinstalling didn't help. Then, hours later, it just came back which is somehow more unsettling than staying broken.
Turns out nothing was broken. The whole UI was waiting on the first mailbox query, that query was politely queued behind the catch-up sync, and the app had no way to say "hang on, I'm reading" so it said nothing at all. For hours. In an empty window. Cool.
An phone app with sync'ed notes could be convenient, but we then lose the co-edit feature on the phone. It's more a quick notes. Eventually we can setup co-edit with the agent on the cloud. So phone can also enjoy the co-edit. Currently leave a todo for the agent on phone is definitely do-able.