Using xfce4-panel 4.11.0 under Xubuntu. This report is either a duplicate of, or duplicates Bug 10842.
I often get hit by applications that, although were working perfectly fine previously, at one point their systray icon simply disappears away. Quitting and restarting the app doesn't make the icon reappear in the Notification Area, which would point to some implementation issues in xfce4-panel. In my case the offending missing icons are for Liferea and SpiderOak.
Also restarting the panel doesn't help things, either.
I have exactly the same issue, five years later :)
Ubuntu 19.04, xfce4-panel 4.13.4 (Xfce 4.12)
Possibly dupe of bug 8451 ? Although in #8451's case, restarting an app will amke it reappear.
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