This is a limitation with the USN Journal and Everything.
Please try forcing a rebuild:
- In Everything, from the Tools menu, click Options.
- Click the Indexes tab on the left.
- Click Force Rebuild.
- Click OK.
Those longer filenames in the screenshot look like they might be the temporary names given to the files, as described above. Maybe those temporary names got indexed by Everything.Transaction based Hardlinking
Before DupeMerge hardlinks file together it renames the file to a temporary name, then creates the hardlink, and afterwards deletes the temporary file. All that is done to be able to roll-back the operation if e.g the hardlinking fails.