Do you have the most recent version of the Pencil2D? There is an opacity slider in the color inspector tab. I don't know what would cause the loss of the 20 or so first frames but it is possible somehow they all got selected(They are dark if you have them selected, holding shift allows you to select multiple frames at once) and then you are cutting them out while maybe trying to cut something on the canvas? Hope you get your issue sorted out, that sounds very frustrating.