Recover from file locations adds ~ on all files

I recently had to do a full hard drive recovery on my laptop. After that completed I selected a recovery for a more recent file based version of my user documents etc.
Unfortunately when it completed recovery Acronis addes hundreds of thousands of files with a ~ at the end of the file extensions which make them useless. I suspect they are actually duplicates of regular files but there is no way I can verify this. It looks like I may have to start over with my recover of the HD and then the files again but how do I prevent the ~ problem? Or, how do I get rid of the ones I already have without deleting something that I shouldn't? Also, the file recover that I have set only backs up items that have changed, so I have versions. Do I only need to recover the last version or do I have to recover all up to the first full version? Thanks for the help in advance.