As far as I know, none of the main features actually use flash. Maybe some of the ads do though.
warning message
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You get pop ups? Haven't encountered those...
I disabled Flash entirely about a year ago. I have no problem using chess.com.
while playing chess a pop up sometimes pops up saying - - - this site ( chess.com ) uses a plugin ( adobe flash player ) that will soon be unsupported - - - so is this a real or imagined concern for people who play chess on chess.com ( chess.commies ? )