Recently I had the same “conflict” updating my EnOS-Gnome system.
I choose to replace power-profiles-daemon but then I realized the options for setting the cpu-scaling in the “control menu” was gone. Also gone were they from the Power section of the Settings:
So I removed tlp and re-installedpower-profiles-daemon.
You could remove tlp prior to update the system to avoid this issue.
Or if you want to use tlp for the power managment of your system just go ahead and replace power-profiles-daemon.