This worked for me earlier:
git checkout HEAD^ etc/miner.conf.donate
git pull
This should also do the trick. All remotely tracked files will be overwritten. Graph data will remain.
git fetch --all
git reset --hard origin/master
If you pulled MinePeon in the last 2 days, you should also pull MinePeonWebUI, check your settings and then save them. The donation code has been updated to use (only) the new settings. If the new settings have not been set, the script will end before initiating a donation.