This bug has been there for ages, and is by far the most annoying (to me at least). I didn’t find any mention of it in the Jira bug tracker.
If, for some reason, Windows Explorer crashes or needs to be restarted, the Spark tray icon disappears, and is not recreated. If Spark was minimized to the tray, the only thing you can do is kill it from task manager and restart it.
Spark shoud listen to the TaskbarCreated message from Windows to detect when the task bar is created, and use this opportunity to recreate the icon. See this page for an example.