I'm not sure about the renaming of files to "[conflicted]", however, never use the "mv" command unless you are really sure what you are doing. It just causes problems. In the future use the program "mc" from the command line to move files between disks and it does not give these problems. You should check it out.
Just type "mc" from the command line and it will bring up a very intuitive interface to copy, move, or delete files. Hit tab to go from side to side. You can also right click on files or directories individually to select them instead of moving, copying, or deleting all of them.
If you do have problems of duplicate files on disks in the future, use the following script to check for duplicate files on your disks, however, I don't think that is your problem at this time since they do not have the exact same names.
UNRAIDFINDDUPLICATES.SH
At this point I would do the move again with "mc" and then after that is completed, I would get rid of the "[conflicted]" files or save them off to another directory until you feel comfortable that all your files have been moved.