I would look into head covers with longer knit shaft protection.

Not sure which hardcovers you use if any but I use the longer knit headcovers to prevent bag rash because I do my fair share of walking. Not sure of any repair techniques.

Try getting some head covers with the long "sock" that covers the portion of the shaft where it rubs on the bag top cuff.

Chris,
A year ago I purchased a Titleist 14 slot deluxe cart bag. I noticed that the material on the club separators was very abrasive. I bought a strip of fleece, some fabric glue sticks, and a glue gun at a fabric shop. I glued the fleece onto all the top separators where the graphite shafts on my new AP1s and Titleist metal woods would rest. One year later I have no wear on any of my graphite shafts.

I don’t think my shafts ever show signs of wear.....but then again I get new ones every 2 year’s!

Long sock is a must in my mind- extra expense is well worth it!!

You will need to do as Norm H suggested, or, get a new, more graphite shaft friendly bag. A golf bag, that causes that kind of shaft damage should not be used.