We have an idea about how to reconcile Repository and workarea when Synchronize thinks all files are the same but we know some of them are out of sync.
1) From workbench select any viewpath and add it to workarea.
2) Edit some files in the workarea.
3) From workbench , select the same viewpath and perform "Compare to Directory" operation. For the client path , provide the project path of the workarea.
4) This will internally checkout all the viewpath files to temp directory and then compare the content for each file.Ultimately, the workspace files will be compared with repository files.
5) As a result all the files with different content will get displayed in sync view in workbench.
Now user can resolve the conflicts with correct content.