Using rsync with parameters -anE --stats --link-dest=/folder/a /folder/b/ /folder/c where /folder/a and /folder/c are in the same filesystem, while /folder/b is in another one, rsync also copies files in c that have different ownership/permissions between b and a, but in "Total transferred file size" statistic it doesn't care about their file sizes
Just a little correction. Evidently using rsync without --stats the correct files are copied, with --stats it just prints wrong stats.