I'm getting some odd problems with the savegames. I saved a game at day 9 and quit for the night. The following evening I found no savegames at all. Quite disappointed I decided to start a new game. I got to day 2, saved and, again, I quit for the night.

Today I cannot find any savegame from Day 2, but the bunch from the previous session, Day 9, are now there, magically appeared from nowhere. It is as if I played with different profiles which, to my knowledge aren't a feature...

I think I'll leave this game on a frying pan until all issues are solved. Combat problems are manageable, but being unable to guarantee my progress will still be there when I get back to it kills the game in its tracks. Which is a shame because the game rocks and I really would like to keep playing but as it is, I ain't no time for restarts.

There is indeed something weird going on with the saves

If you play the game online with gog galaxy or with galaxy running in the background your saves are saved here (appdata is a hidden folder)

C\users\*yourusername*\appdata\local\PhantomDoctrine\saved\*folder with a bunch of numbers*

But if you run the game without galaxy running AT ALL, yours saves are here

C\users\*yourusername*\appdata\local\PhantomDoctrine\saved\0

You can move your "online" saves to your "offline" folder "0" or vice-versa if you want to restore your progress.
As you can see your saves aren't deleted, they just won't be detected depending on how you launch the game, then make sure you are either running

"offline" -normally through the game .exe in your install dir, no galaxy running at all.
or
"online", through galaxy or galaxy running in the background.

Choose one method or you are going to have to manual move one save to another

That's just it, thanks mate.