I currently have a hard drive that I backup using RSync. I do weekly; monthly snapshots. I would like to compress some of my hard drive using NTFS compression. How would that affect my future snapshots? I am not clear if my future snapshots would use hard links the same way or it will create an entire new backup.
Do you really need to use NTFS compression?
Maybe will be better to compress with .tar.tgz using --rsyncable option. It will only send the differences of .tar.gz and will save network bandwidth.
If you really need more compress level, you can use gzip -9. And if you really need save more space, you can use rdiff-backupt to save only the differences (you have to preserve original file to recover). I do not recommend rdiff-backup because if you lose original file you will be in trouble.
When a filesystem provides compression it is usually intended to be transparent, so that there should be no difference between the original file and a compressed version, apart from some meta-data such as the actual number of physical blocks used. This would seem to be the case with Linux NTFS-3g.
By default rsync only compares timestamps and sizes of files to decide if they are unchanged. Note, only new (i.e. different) files will be compressed.