Hi,
I'm having the same problem - sort of.
I just installed Win 8.1 and Created a Recovery USB Drive before I installed anything.
Since then I loaded files and added partitions. The hidden files are still there in the Recovery partition, but somehow Win 8.1 can't find them... I noticed the volume name disappeared. Don't know why or how it changed...
I use EaseUS Partition Master to backup my MBR and Boot files. It may not give me the tools I need if I need to diagnose HD errors like Win 7 tools.
Will try to boot off the USB and CD later to see if it works... Will also check to see if I have a restore point...