Encryption Software and recovering files

I work on a rather large enterprise. We have recently installed an encryption program that encrypts the entire drive. During some of the installations it has failed or even afterwards the encryption becomes corrupt. We have one of two options, attempt a decryption(95%) failure rate, or reload the box. I am wondering if anyone knows of a way around this? Has anyone ever seen an issue like this before? The other thing is we divide our hard drives into two partitions, one for OS and applications, and the other for user data. If we just blew away the partition with the OS and applications would the encryption still reside on the second partition? I have been attempting a to blow away the first partition and hook it up to a sata to usb and create an external drive but no such luck. It keeps telling me to format the drive. If I run a CHKDSK /F it shows me there is in fact data on the drive. I also tried to reload the OS on the first partition and see if it would pickup the second partition. This also yielded the same result of do you wnat to format this drive. Any and all help is welcome and I hope someone has a better idea than I do.