I agree with Phillip, that you need to back up your photos that are irreplaceable, but make sure your put the flash drive or portable hard drive in a place that doesn't get vibrated, such as a safe. Although, I would suggest putting them onto a CD and putting that in a safe place because I have yet to see a CD fail from using it.
Now to try and solve the problem that you are having.
Are you sure that all of the pictures that you have, your phone will recognize them?
If so then one of two things may have happened. Your files are unfortunately corrupt or the phone is having a problem showing all of the photos.
Have you had that SD in a different phone, such as an IPhone? If so then the pictures you had taken with it may be a different file type and is possibly the reason they are not showing?