Every time I login my application menu's favorites are empty. I can add favorites and will remain there as long as the session is open. But as soon as I log out and back in again, the favorites are all gone again. This seems to be a regression in either 5.13 or 5.13.1.
Apparently deleting ~/.local/share/kactivitymanagerd/resources/ and ~/.config/kactivitymanagerd-statsrc fixes the issue: https://forum.manjaro.org/t/kde-can-t-add-favorites-to-app-starter-menu/33538/13?u=atharvalele
Have Plasma 5.13.3-1 running on Arch 4.17.8-1. If I mark an item as Favorite, it will show up on the Application>Favorites menu for that session, but will be gone on reboot. Deleting ~/.local/share/kactivitymanagerd/resources and rebooting to recreate it seems to work, now I also have History back.
I had the same problem and the same solution did help.
I have Archlinux kernel 4.18.6-arch1-1-ARCH and plasma-desktop 5.13.5-1. As ikidd3123@gmail.com, deleting ~/.local/share/kactivitymanagerd/resources and his content, logout from session and relogin again solved the issue. Also I have history back.
This was fixed a few releases ago due to some activity manager improvements.