Just to let you know, I have a fix for this issue now, and it was fairly simple in the end.
I'll try to tidy it up and publish it in the next week, hopefully as part of the Eternity Keeper save games editor.
Meanwhile if you wanted to send me one of your new format saves I could test if my fix works for you too.
Update: thanks to those Steam users who've confirmed my savefile fix works for their Windows Store save files.
It would be nice to have a GoG user with the same issue volunteer to test a converted save.
Also, it turns out my initial fix only works for the character state. There is a similar issue with the level state still needing to be fixed. The only negative impact so far seems to be that some enemies (and items?) respawn. A fix for that will be more involved to implement but I think I know what's needed. I may publish before that's ready depending on how much progress I make.
Update 2: an alpha release of Eternity Keeper with Windows>Steam conversion functionality is now available for download from https://github.com/ktully/eternity-keeper/releases/tag/0-20.a
Instructions are at https://github.com/ktully/eternity-keeper#converting-windows-store-save-files-to-steamgog
This fixes all the issues I'm aware of, including characters loading corrupted, and the level respawn issue. Let me know how you get on with it.