I just had this exact same issue on a new 50CM2.
The 2 throttle levers and the flaps lever were still working, none of the other buttons were.
Check if there are any SPI errors in the config tool. (Button page)
The cause of my problem ended up being a connector having pulled free inside 1 of the levers.
If you turn on the debug mode and uncheck 'check for spi errors' some buttons should start functioning again if this is the issue.