How can I upgrade from elementary OS Freya to Loki without losing my data, you may ask?
There continues to be no officially supported way to upgrade between version of elementary OS. This is due to the installer being a patched Ubuntu/Debian installer with no custom elementary support for upgrades, only detection (which I believe has been upstreamed).
Clean installation is the recommended method, this creates a new working environment and removes any config conflicts commonly encountered when keeping an entire home partition.
Upgrading though the update manager is not even possible, the update managers vary between these versions and this will never be made available. Any upgrade offer you see there is for the Ubuntu backend, not elementary OS.
Upgrade from installation media works much like installing cleanly does, only you leave your data on the disk as well as making a backup. This is untested and results will vary significantly. If you experience any issues, the likely response will be "does this happen on a clean install?"
- Back up everything
- Make some Loki installation media.
- Boot from the install disk and select the "upgrade" option.
Source: Me, I wrote most of the installation guide.