Hello bbbbobbb,
Thanks for the post in Apple Support Communities.
If I understand correctly, when you click a phone number in Safari, it opens Skype and you don't see an option to change this. Is that right? Do you still have Skype installed on your Mac in Finder > Applications?
Checking your FaceTime preferences was a great idea, since that setting does affect how phone number-formatted URLs behave: Change preferences in FaceTime on Mac. If you don't see the "Default for calls" option in FaceTime > Preferences, try clicking Sign Out in FaceTime. Then, sign back in and see if this helps.
If it doesn't, try clicking Apple menu () > Restart and then test it out.
You mentioned you're running the latest FaceTime version. Are you also running the latest macOS software? If you're not running macOS 10.14.2 there, updating your macOS software is a great next step:
Back up your Mac with Time Machine
How to update the software on your Mac
I hope this helps!
Cheers.