It happened just today after downloading the free "Like A Dragon" DLC content. Haven't played the game in a few months, but have 22.2 hours on it, having completed at least 5 runs and made good meta progression. For some reason after the download completed, the game started up, opening the first title screen. I pressed a button, then it went to the screen with the "Go to Saloon" option. Pressed that getting into the saloon walk around area. Thats when I realized after checking the Library in the bottom left area that all my progression was gone, as if I just started the game. Also, the only characters I have are Sweeper, Zed, and Bunker, and I only have one District unlocked.

I looked around in the setting to see if there was something that could explain what happened. All I saw was the "Reset Profile" option in gameplay, which I know for certain I have never pressed. 

So for some reason, whether with this or another update, my progression was reset. I'm not sure if there is a way to recover it, but I'm baffled as to how this could have occurred.