me@mypc:~/temp$ mkdir original backups backups/snapshot1 backups/snapshot2
me@mypc:~/temp$ touch original/FileKeep original/FileRemove original/FileExclude original/FileNewlyExclude
me@mypc:~/temp$ ls */*
original/FileExclude  original/FileKeep  original/FileNewlyExclude  original/FileRemove

backups/snapshot1:

backups/snapshot2:
me@mypc:~/temp$ rsync -a --delete --delete-excluded --exclude=FileExclude $PWD/original/ $PWD/backups/snapshot1/
me@mypc:~/temp$ ls */*
original/FileExclude  original/FileKeep  original/FileNewlyExclude  original/FileRemove

backups/snapshot1:
FileKeep  FileNewlyExclude  FileRemove

backups/snapshot2:
me@mypc:~/temp$ rm original/FileRemove
me@mypc:~/temp$ touch original/FileNew
me@mypc:~/temp$ rsync -a --delete --delete-excluded --exclude=FileExclude --exclude=FileNewlyExclude --link-dest=$PWD/backups/snapshot1 $PWD/original/ $PWD/backups/snapshot2/
me@mypc:~/temp$ ls */*
original/FileExclude  original/FileKeep  original/FileNew  original/FileNewlyExclude

backups/snapshot1:
FileKeep  FileNewlyExclude  FileRemove

backups/snapshot2:
FileKeep  FileNew
me@mypc:~/temp$ find backups/ -name FileNewlyExclude -delete
me@mypc:~/temp$ ls */*
original/FileExclude  original/FileKeep  original/FileNew  original/FileNewlyExclude

backups/snapshot1:
FileKeep  FileRemove

backups/snapshot2:
FileKeep  FileNew