Each Real-Time Save file takes up between 4.5 to 5MB (ouch!). So it is quite a lot of space compared to regular saves, which are only 512KB large.
This is why you must hold Select to create a real-time save file, otherwise you're MicroSD will become very cluttered.
I don't know if the Cyclo will alert you when you have no space left for Real-Time Save, but if the saves suddenly stop working then it's probably time to clean out your MicroSD.