It seems to keep two versions in its one save file or just hold the last "checkpoint" state in RAM. The checkpoint state seems pretty random to me. Sometimes it's the last inn you rested at, sometimes it's a quest autosave, and sometimes it's a area transition autosave.
To load the manual save you need to exit to the main menu or to desktop and then select load game from the main menu.
The save system in this game is absolute garbage and have cost me a few hours of progress here and there too. Especially the way it will autosave after you fail a quest. That's just rubbing salt into the wound...
I'd recommend this mod to in order to keep save backups.
http://www.nexusmods.com/dragonsdogma/mods/96/?
Copy the two files into the main game directory and then edit the ini file to set the number of saves you'd like to keep and to manually set GOG's save file directory:
"C:\Users\YourUserNameHere\AppData\Local\GOG.com\Galaxy\Applications\49987265717041704\Storage\Shared\Files"
To restore an older save exit the game or exit to the main menu and alt-tab out. Then go to the directory above, find the file with the timestamp you want, make a copy of it, delete the delete the current save, DDDA.sav, and rename the copy DDDA.sav. Also be sure to use use caps as show otherwise the same won't read it and will start a new game for you. You can always close the game and fix the name if you make a mistake.