If you know that all the files have hardlinks within a single directory hierarchy only, you can simply do

find inputdir -type f -links +1 -exec rm {} \; 

The reason this works is that rm {} \; removes exactly one file immediately the stat() returns count more than 1. As a result, the hard link count of the other parts of the same inode will be increased by 1 and if the file is then the only copy, the rm will not be run for that last file by the time find runs stat() against that file.

Note that if any file has hardlinked copies outside the inputdir this command will remove all copies within inputdir hierarchy!

If you know that all the files have hardlinks within a single directory hierarchy only, you can simply do

find inputdir -type f -links +1 -exec rm {} \; 

The reason this works is that rm {} \; removes exactly one file immediately the stat() returns count more than 1. As a result, the hard link count of the other parts of the same inode will be decreased by 1 and if the file is then the only copy, the rm will not be run for that last file by the time find runs stat() against that file.

Note that if any file has hardlinked copies outside the inputdir this command will remove all copies within inputdir hierarchy!