Trouble saving larger wave files (4 bar)

I'm using JJOS2XL and have been recording 4 bar audio loops from my Prophet 600 to the MPC. I'll use Pad 11 to record the track so everything syncs, then I'll just add it as an audio track. I have a hard drive installed and have tried saving these samples to the hard drive individually. Then I'll save all as I usually do with my project. The files are never there though even though they say they saved. Anyone have any ideas on why these files keep disappearing and what I can do to prevent this?

Have you formatted the drive within the MPC?

do that if you haven't.

Yeah I have a lot saved on the MPC. I even just deleted some larger files that I wasn't using and now it allows me to save my own large samples again. What would be the purpose of formatting the hard drive?

If the drive hasn't been formatted within the MPC, it can be erratic in lots of ways, even though it may seem to be working sometimes.
Same with a memory card. It needs to be formatted the way the machine expects it to be formatted.

Try this:

Go to save mode, create a new folder and save ENTIRE MEMORY to that folder. Are the files then there and do everything work once you load the project file (PRJ)?