I reckon I'm somewhat late with starting a thread here, but I'll try anyways. 

Summary: 

I seem to have access to different saves depending on how I launched the game. I don't know where they are, either. 

Background: 

Yesterday, I bought The Lost Tales DLC, then, upon the game not launching anymore, I verified the game files, and as I then couldn't load saves anymore, I reapplied the community patch. I launched the game, loaded into a save (without the new DLC active, of course), and started playing. 

After an about ~1 hour break, past midnight, I went to save and noticed the saves list was supposedly empty. I checked on Steam Cloud, and it was empty as well. So I saved once with Steam Cloud active, then deactived it and saved again. Both of those saves showed. 

I played on and saved; the loss of the old saves would be annoying, but acceptable. 

Situation: 

~11.5 hours later, I launch the game, through Steam, and, *drumroll*, there's all the saves from pre-Midnight, the old saves, and none of the new ones. Nothing in the cloud, either. 

Last save was shown as from 22:48. 

Finding the save location for the game at C:\Users\%USERPROFILE%\Documents\Endless Legend\Save Files, what do I find? 

All of the new saves. 

I closed the game, started it from the exe in the game folder, and I get the new saves, including the one in the steam cloud. 

So, it seems if I start the game over steam, I get one set of saves, and if I start the game from the folder, I get another set of saves, both complete with their own steam cloud. Maybe they think they are different versions? 

The question remains, how did I manage to get from one to the other, as the new saves are the continuation of a (running) game from the old saves. 

Also, if anyone could tell me where all those other saves I see when starting the game from Steam are, I'd be much obliged. Steam cloud is not set active, so at least some of them should be somewhere on my machine.  (starting from the folder also doesn't keep my steam ingame settings, so I don't think I did that yesterday)

System: 

Windows 10

I didn't put this in Tech support as the main 'problem' has been solved;  (edit: Maybe, upon rereading, Tech Support would be the better place)
I can keep playing like this, but it is odd. But I do feel uncomfortable having saves in 3 different locations and being unable to locate one of them. 

I'd be appreciative of any info on this, or simply a hint of where I might have failed to look. :)

[edit2: I just encountered this again, I started a new match through steam, I go away for an hour, and when I come back and try to save, I'm back at the new saves, and none of the others. 
I do now believe this belongs in tech support. I'll also ask somewhere else.]