So basically I randomly have icons that disappear, when on the desktop or the task bar.
First time I had this issue, was with MSI Afterburner. Then re-installing worked - for a while, until it suddenly disappeared again. Now it's FFsplit that does the same. I downloaded it yesterday and it was fine, when I turned on my computer today, same thing had happened and the icon was gone.
I have no idea what causes this issue and it doesn't seem to be tied to any specific action.