Using the TopIcons Plus Gnome Shell extension, some icons disappear from the system tray after the system sleeps and wakes up again. However, the applications’ processes are still running.
How to prevent this?
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There isn’t any good way to prevent it. Shell shuts down extensions whenever the lock screen activates, by design. Annoying, annoying design.
My suggestion:
sudo dnf install libappindicator libappindicator-gtk3
That’ll install support for the AppIndicator system developed by Canonical for Ubuntu’s Unity desktop, which works far better than the broken shards of systray support left in Gnome Shell. In my experience most applications that support a tray icon will use AppIndicator if the library is available, and it often works far better.
(It’s the difference between a Dropbox icon that’s usable and one that kind of isn’t, for one thing. In my experience the Topicons relocation of Dropbox’s systray icon has interaction issues even when it is visible. Dropbox’s AppIndicator icon has no such troubles.)
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Oh, and for any stragglers that do only support systray, you should also switch from Topicons Plus to Topicons redux, which works better under F29/F30. It still won’t solve the lockscreen-death problem, though.
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I tried this and disabled TopIcons Plus, but no systemtray icons appeared even after a restart. Is there any configuration needed?
It happen to me too, I open a Bug Request in BugZilla, you can add you there as cc and track the bug, because you have a FAS account too:
https://bugzilla.redhat.com/show_bug.cgi?id=1714033
Regards.,
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My FAS account is also bugged… I still can’t log into Bugzilla with it.
To confirm what @ferdnyc said , the icon disappearance happens after the lock screen. Of course since sleep also locks the screen, it happens in that case too.
Also, it affects only some icons. Unaffected icons include dropbox, pidgin, dnfdragora.
So @ferdnyc’s suggestion of using AppIndicator support also needs the installation of this Gnome extension: GitHub - ubuntu/gnome-shell-extension-appindicator: Adds KStatusNotifierItem support to the Shell Now it works… sort of. Pidgin doesn’t work with it. 
Ugly workaround solution to get 1) persistent icons after screen lock, and 2) get all icons (that I’ve tried) showing: use both AppIndicator and TopIcons Plus extensions.
I also tried TopIcons redux, but when set to the right side, it is positioned at the very right, beyond the default Gnome indicator area… why… TopIcons Plus when positioned to the right is still to the left of the Gnome indicators, which is my preference.
One thing I don’t like about this AppIndicator solution: clicking on the icons just brings up a context menu, same as right-clicking, instead of actually bringing up the relevant application window. More clicks to get the same result. It’s annoying, but maybe makes sense for touchscreens.
Also, am I the only one who really dislikes the idea of managing system components like extensions through a browser?? And the elimination of basic functions that were present before, now being relegated to third party extensions??