Initially, all found invalid entries are marked as "Delete the entry". Then Registry First Aid searches the hard drives for corrections and decides what correction is the most appropriate for each entry. Registry First Aid makes the decision about which entry can be deleted or not after all available corrections have been found.
If they are then unchecked, it's because they are too complex to be determined what you need to do and they require you to analyze what to do with them. If they look like some sort of system item, it is recommended to add them to the excluded list to leave them intact and not check them in the future.