In my first season, I've learned before I boot up the game to do a file integrity check. All the time when I do this check I get the same message...three files have been found invalid/missing, will reacquire.
I notice that when I am in the 2d game mode, at sometime the sound gets "funny" (reverbration, muddled etc.) At the end of the game when I quit the game summary screen, the in game sounds do not stop. They remain playing even when I am at my dashboard, etc. Latest version on WIN 10. I don't know if this sound is the problem with the three files missing.

You should a Support Ticket, sending your game files along with your explanation of what's been happening. Go to HELP within your game screen for instructions on how to do this.