Computer and external issue !!!!!?

I have been using a program called magic dvd ripper to rip dvds to my external. I have only been using one laptop to do this. Last night my laptop updated automatically. This morning it was still updating so I left it be I got back from work and started up my computer and I had noticed that it had deleted folders and pictures off of my external. so I restored my computer back to yesterdays date. Here is the thing when I opened my external the deleted folders were there for about 5 second then they went away again. I have restored two times and they reappeared both times but then went away. I need to know how to get these back it has also made some files in the external non operational they say that they are corrupt. HOW CAN I FIX THIS it is very important I have lost over 3000 family pics.