Cecile is pregnant, and Joe could have another kid by the time The Flash presumably returns for Season 5 next year.
His breakup with Jesse upset him so much that he feels the need to get away from Team Flash for a while, and there’s no saying how much time he’ll need.
One of Joe’s kids left just before he discovered that he might have a new kid in the not-too-distant future.
Interestingly, the bombshell that Cecile is pregnant came in the same episode that Wally made the decision to leave Central City (and Kid Flash) for a time and stay with a friend in Blue Valley.