Matt... The GAO notes that you do indeed record a score for the hole for handicapping purposes. This is from their FAQ on Handicapping:

Q: What score do I post for holes that I didn’t play, or didn’t finish?

A: Under the Handicap System, each player is required to record a hole score for a hole not finished, not played, or not played under The Rules of Golf.

When a hole is started but not finished (including conceded strokes), the player must record for handicap purposes the most likely score. The most likely score consists of the number of strokes already taken plus, in a player’s best judgment, the number of strokes that it would take to complete the hole from that position more than half the time.

Hope that helps :)

Matt what our group does is pt down a score that would be appropriate for the circumstances. The last player has a 20 foot putt and picks up we would add 2 strokes to the score as highly unlikely he will sink the the ball on a one putt. If by chance the player has a 2 foot putt and picks up add one stroke as he will in all likelihood make that putt. It is never going to be accurate unless the player putts out.

Hope this helps.

Thanks, appreciate it. It's a hard thing to tell your buddy to putt out and when they are a bad putter it makes things even more awkward HA!