I'm assuming you have done the work getting an icon onto the system tray.
Due to the proprietary way in which PB handles resource, the only icon which is available (easily) is the application icon. You can get that using ExtractIconA(...) or LoadIconA(...) but that's it. If you want to make a blinking (animated) icon then you will need to take a different [read: clunky] approach: create a C++ .DLL [you can use an .EXE file but that is a temptation to users] containing the icons you want to use, then use ExtractIconA(...) to get the icons out of that to display in the system tray. The main downside of this is an additional file to deploy and you will need to code some back up to display a default icon in case your icon library .dll goes missing.
Once you've done that, you can use a timer event to cycle through the icons involved in your animation.
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