What's suspected is that when applications are upgraded, the shortcut is removed and added again in a way that Plank only thinks that a removal has occurred. The best known workaround is to create a copy of the launchers, or to re-add the affected applications to the dock after update.
There's a thread of Manjaro linux users who have the same problem:
https:/ /forum. manjaro. org/t/icons- dissappearing- from-plank- after-updates/ 43740
What's suspected is that when applications are upgraded, the shortcut is removed and added again in a way that Plank only thinks that a removal has occurred. The best known workaround is to create a copy of the launchers, or to re-add the affected applications to the dock after update.