botched clone?
 

I cloned a Hard drive using acronis, it informed me that it completed successfully. I attached the clone i had just created to my system and booted up, I was able to open several files, and everything looked intact. On the original system I then used the built in recovery partition to wipe the source drive and reinstall the OS. I then went to copy the data from the clone I had created, but the folder i need is named < a bunch of ascii squares> and the folder contains nothing. I did a data recovery on both drives and couldnt find the folder. Im trying to wrap my head around what could have possibly happened. The only thing I can think of is that the folder was encrypted, and I dont have the software inplace to read the directory properly now.

Does anyone have any input or suggestions?

If it's encrypted, you have the certificates, right?
So it's all ASCII characters or just letters and numbers? If just letters and numbers, it could be a hidden update file, which when you copied it, might have somehow lost its system/hidden flag.

If you used CLONE mode in Acronis it does not matter if you have hidden or encrypted files, partitions or whatever - because it is a bit for bit copy rather than a file copy - it basically does a mirror copy of your HDD's sectors - so your destination drive should match your original.

The thing is I wasnt made aware of anything special going on with this drive. The folder i need is in the exact directory tree location that it was while the OS on the drive was active. Yep it looks like a bunch of ascii squares. I dont have any certificates. Im going to try cloning back to a sata notebook drive, and booting from it and see if any certificates that might have been in place kick in.

Well only you would know what was on your drive.
Is it a specific file you had special info on?
if it isn't who knows
Its pretty hard to say really for 100% sure without being there and seeing everything.
Is it effecting the operation of the clone drive or the new OS drive without its access?
Maybe a protected file-+ who knows?