Did you delete the config when you updated? Wouldn't it keep the old setting if you didn't (decay has always been an option, but it just recently became the default behavior of Botania)? Although, if that were the case any new passive flowers you put down would stick around as well (no idea if you've put any new ones down, obviously.)
Given that it's a config that you can change in-game, I don't think it's a big deal (though I don't really use much passive generation beyond the very beginning of a world.)
Given that it's a config that you can change in-game, I don't think it's a big deal (though I don't really use much passive generation beyond the very beginning of a world.)