The tool just rename the original file and move the, in system temporary folder, created one to the directory of the original, giving it the same name. Because the backup file, and new one, are equal, and because you say that even when rebuilding the index the new one don't get indexed, I really don't have a clue for what's going on.
Can't be an ifilter file compatibility problem, because files are equal. The only thing that is left is file access rights (and this is compatible with moving file to another disk and back on), because an index rebuild should include any file, so a possible bug in the indexer code that identify what files need to be indexed is not a possibility here. Do you know if the indexer service, or the Adobe ifilter, can log to file?