Factorio suddenly doesn't like spaces, neither in game path, nor in save names.
How I got this, is really confusing, so I am posting this in whole:
====== 8< ============================
I have these folders:

Notice, that there is both Factorio and Factorio 0.17 folders - the former is 0.16.51 install, 0.17 is separate one for testing.
This is what I thought was the issue at first!
Next, I add some random mod, let the game restart, and sync a save with the mods...

After restart I am greeted with following message:

Notice the path!
Then I land in the main menu.
After few tries I usually end up in the game, and everything looks to be working, though.
Then I rename the folders with other installations:

Try to sync save with this mod again, and...:

removing and readding the mod still gives me the last message.
Finally I change the folder name to include underscore instead of space:

And while synchronizing I get this:

But wait, the name of the save... yes, it has a space!
So I quickly loaded the save (without sync), and resaved it:

And presto:

Conclusion: don't use spaces.