Apple partition map/GUID backup issues

I was cleaning up (storing, moving, deleting, renaming etc.) some files on an external hard drive and when done I backed it up as usual using Chronosync but got some strange behaviour. I believe there was some filedate discrepancies (a newer file is found on the destination drive) that led me to see there were files on the source drive that I had never heard of before, so I clicked on Chronosync's "analyze" button and could see the following files (in addition to the usual visible and invisible ones):

.DocumentRevisions-V100-bad-1
.vol
.PSInstallSandboxManager
automount
bin
bin (Mac OS 9)
cores
cores (Mac OS 9)
Desktop Folder
dev
etc
etc (Mac OS 9)
mach_kernel
mach_kernel (Mac OS 9)
network
private
sbin
sbin (Mac OS 9)
TheFindByContentFolder
TheVolumeSettingsFolder
tmp
tmp (Mac OS 9)
usr
usr (Mac OS 9)
var
var (Mac OS 9)
Volumes
Volumes (Mac OS 9)


Furthermore I checked both drives with Disk Utility and found out that the source drive used the "Apple partition map" while the backup drive used the "GUID partition table". Both drives are "Mac OS extended (Journaled)" formatted and have owners enabled (I've also tried disabling owners).
The source drive has the "Verify disk" and "Repair disk" buttons in Disk Utility greyed out, so that's not possible (it is however possible if I select the drive partition). At some stage I got an error message saying "Error: Live file system repair is not supported" and this happened with the destination drive as well. So what's all this about?

I'm thinking that I might have formatted the source drive years ago and somehow selected compatibility with Mac OS 9, so my thought was to back up all the files, taking care to exclude those system specific files (listed above), then reformat the source drive to delete all that Mac OS 9 stuff and finally copy back all the files. But now I see the destination drive also has those files, and I even used Chronosync's "Mirror" backup method and deselected the OS 9 files.
What should I do to make the drives normal again without losing my files?

 

Never mind....
I copied the entire drive, then deleted (using the terminal) the various invisible files on the backup drive and finally reformatted the source drive and copied everything back using Chronosync.