Do the following from the Updating Sailfish OS article:
Final clean up
The OS update notification may persist in the device after updating the OS with the command line method. The commands below may help in eliminating the notification:
cd $HOME
devel-su
pkill -f osupdateservice
rm ./.cache/sailfish-osupdateservice/os-info
You’ll then see the proper version in the Settings → Sailfish OS updates. However, checking for an update will revert to the 5.0.0.78 update, which I’ve been told is a bug.