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It sounds like when you did the Save to Disk operation, you didn't have enough free disk space for the new copies, so many ended up with 0 size. If so, there's no way to fix those copies, and you'll need to get the originals back. You'd better remount the disk as read only if you want to try some undelete software to recover them, because if you still have little free space on the disk, then each new file will be overwriting the blocks from those deleted originals.
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