It is pretty doubtful that you will weaken the spine of a carbon arrow enough that even a hooter shooter could notice the differene.

One thing you should try is chaning the nocks. Nocks can and will wear out over time and can lead to some erratic arrow flight.
If that still does not help things, try turning the nock 120degrees to the next fletch. Sometimes the spine in one part of the arrow can be different than another, resulting in an arrow or arrows that will not group. Turning the nock in most cases will pull the arrow into the group. If it does not, advance the nock to the next fletch and try again.