Disk version saves (started in 1.0034) are not compatible with the download version of the game; people have reported either that the game crashes trying to load, or that they can load the save but then not save afterwards. Saves started in earlier disk versions are ok, but I think with the 1.0033 patch there was a change made in the inventory file format that causes a problem with the download version of the game. If there is ever a patch, though, presumably it would update the download version to be able to recognize the last disk version save format.
A couple people who lost their Play CDs were able to get up to the Blessing Ceremony in the disk version (where a cutscene requires the disk), then replace their inventory files with ones from my first game (started in the original release) and then continue in the download version. Swapping inventory files at any other place in the game would very likely cause problems with missing quest items, etc. It is also possible to use files from the download version of the game to create a replacement Play CD (virtual or CD/DVD-R/RW).