If some one leaves the site their photos are taken down. The only way you can prevent that is to copy the photos to your own photo file, and perhaps then put them in a hidden photo file

I believe that there’s also an limit on how many favorites you can have. I seem to remember that it was increased a while back, but it’s still something like 2,500. When you reach the limit, the oldest ones disappear from your list.

Yes, know this problem. I think the reason for this (if user or pic didn't get deleted) is that the status of the pic got changed, e.g. from public to friends or private and back.

Users deleted pics and vids themselves.
or
They've deleted their profile resulting in their pics and vids being deleted too.
or
They've been idle for months resulting in their profile being deleted automatically.