So sometimes when I suppress several features using Configure Feature my model gets angry and warns me there are lost references.
I check the model and the sketches for the features I just suppressed are unsuppressed and looking for the features that are no longer there.
I suppress the sketches and *tadah* everything is fixed.
Why would a sketch not follow the suppression of the feature? Sometimes it works sometimes it does not.
So after so trials I realize sketches do not suppress with their feature, but they do suppress with other features and other sketches if they use them as references. I also found out that you can use the same sketch in multiple features, which would be why the sketch doesn't suppress when the features does.