When loading up a set (from Live 5, but 'saved as' a Live 6 project/file) and samples are missing, I use the new 'Missing Files' menu, set the folder, and go. Live locates the files, puts up a dialog box "60 files were found, 59 files replaced' or something like that, I hit 'ok', and the program crashes.
When I drag an original file into session view from the file browser into the slot where the missing file is, the file loads just fine.