You never get a signup bonus if you don't apply for the card "from scratch". No signup bonus if the bank converts you, no signup bonus if you product convert the card yourself.
however, the signup bonus on the Freedom card is puny (max 10k in recent years). If you just follow the rotating bonuses and use this card just for them, you can probably outdo the signup bonus pretty quickly. Between 10x points on Amazon 4Q 2015, 5x grocery, 5x gas, and 5x restaurant bonuses so far in 2016, without doing anything other than my ordinary spend in those categories, I've earned more than 15k UR points in the less than a year since Chase converted my AGR card to Freedom.
So aren't you shooting yourself in the foot by not using the card just because you didn't get a tiny signup bonus???
Evaluate how much the rotating bonus could earn you, and compare that to any other cards you have, and evaluate whether to keep it that way, not based on some tiny bonus you missed out on because you decided not to apply for this card before Chase auto-converted you.