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The same happened to me 3 weeks ago. Chess.com said the were doing an upgrade but I still lost the games on time.

This shouldn't really happen because usually when the Live chess gets disconnected, it shows the wait indication over the entire screen.
This might be specific to a device like an iPad - were you just able to type & send messages, or were you also able to read new messages from the opponent while it was showing the game as disconnected (maybe that you were typing and sending messages but nothing actually reached the opponent)?
I guess server problem