I've been a practicing registered dental hygienist for 11 years. Once a cavity has progressed through the enamel to the next layer called dentin, it is NOT reversible and spreads quickly as it is much softer than enamel. If these cavities were diagnosed (especially with x-rays which leads me to believe they were inbetween the teeth) then I'd definitely get them fixed. They only get worse not better. It's impossible for a cavity to disappear that has gone through the enamel. You may have seen some food debris or something when you looked in her mouth before and saw a brown spot or just can't see it anymore due to lighting or angle or something. You can always have the dentist show you the cavities again before they get filled to make you feel more comfortable about it. DON'T just let them go! You don't want to deal with a pulpotomy (baby root canal) when it could have been a simple filling.