Program won't load sample even though it's right there.

Mpc 2500 jjos 3.12, full ram 40gb harddrive, I made a program and then accidentally saved it to the hardrive itself as opposed to in its proper folder. I deleted the stuff outside the folder, but the program won't load the correct samples and gives me a file not found. some of the samples work but others I need to load manually everytime I want to use the program. Is there anything I can do to get the mpc to recognize that the sample is in the same folder? I tried renaming the sample and using that on the program, but it still won't load. I just can't spend 10 minutes programming it every time I turn it on.

To clarify, the samples in the folder with the program are all functional, I can play them and put them back in their place, but when I save and reboot the machine, it doesn't recognize what I just did.