This is what I did, hopefully it works for you - I had a similar problem. I would try to load a previous song or whatever and it would just say files and samples don't exist. So this is what I did...
Search your computer for the format that all your old projects came in. With Maschine it is .mprj - take those and put them into one folder on the desktop. Then seek out all the .wavs (samples) and place them into another folder on the desktop. Open Maschine, go into 'disc' and rescan both of those folders.
Now you will most likely find duplicate copies of your projects in the maschine browser, but one will work and one will not. So you open the one that does and save it right away, and delete the empty file.
I'm not sure if this applies to your exact situation, but it worked for me.