I used the following:

1. built in backup to SD
2. ssh as root; tar -cvf /media/mmc1/backup.tar ~user

Then I reflashed, restored the built in backup, and reinstalled my apps.

After that:

cd ~user; tar -xvf /media/mmc1/backup.tar

Reboot.

Everything works well after that. Don't be too scared of the reports here that nothing works. Most people do not have any issues, but those who have make lots of noise.