Will Windows 7 Error Check Program be able to process the Acronis Secure Zone etc.

I use my computer all day every day. I have a new computer with Windows 7 Home Premium with a Seagate external desktop drive. And I have an Acronis True Home Image 2011 program. After about a year of use, this window came up suddenly with a tab in it Perform System Maintenance. So I decided to click on the perform tab.
It subsequently said that DISK VOLUME ERRORS WERE DETECTED.
I was advised to run CHKDSK and I did so twice over a 2 week period. CHKDSK took ages to finish its 5 stages. It then restarted my computer automatically. When windows fully booted, I ran System Maintenance program again to check but the disk volume errors were still detected.
I subsequently realized that when I disconnected my USB external hard drive and then booted my computer, no disk volume errors were reported.
So it is very likely that my Seagate External Desktop drive must be faulty.
Before I try to fix errors by right clicking on the external drive, selecting Properties> Tools > Check Now, I am concerned about the following.
If I tick the 2 boxes for "automatically check the file system errors" and the other box that says "scan for and attempt recovery of bad sectors", will this affect my documents, videos and music files ? Will this affect my Acronis backups? They are in a 150 GB Acronis Secure Zone partition in my external hard drive.
Also will the Check Error program be able to process the Acronis Secure Zone?
If my backups could be damaged, how can I transfer them onto a new folder in my C drive ?
Thank you for your time and expertise.