I have done lots of successful Alix 2D13 updates remotely across a functioning OpenVPN link, although all the recent ones have been from 2.1-BETAn to 2.1-RELEASE, since I was using 2.1-BETAn for some time, and I use the 2G image. The system reboots and OpenVPN re-establishes.
There is no need to do "duplicate slice" before upgrading. The upgrade will write the new version on the slice you are not currently using, then switch boot slices and reboot. Perhaps you are duplicating slices, switching the boot slice, then not rebooting - or some unusual sequence that then causes the upgrade to not write to the expected place?
If it comes up in factory defaults, then that implies config.xml has got lost, corrupted or??? That is on a separate CF partition, separate to the 2 boot slices/partitions.