Everything you eat can have good and bad effects. That a new good or bad effect to some particular food may be discovered in the future does not invalidate those discovered previously.
I'm sorry, but this is the wrong explanation. The right explanation is that doing nutritional research is hard and that nutritional claims are often not well-supported.
There was never enough proof to say "Fat is bad for you", nor is there currently enough proof to say that "Saturated fat is bad for you". Besides being instantly suspect by being ridiculously simplistic, such claims are almost exclusively based on correlations or effects in high-risk groups. But people really want nutritional advice, so somebody is going to give it to them, citing some paper that suggests some effect.
Don't get me wrong: There are some things where the causal relation between it and a negative health effect is known, but in nutritional advice that generally is not the case.