hww@my-domain:~/workspace/rsyncbug$ ll
total 36
drwxrwxr-x 4 hww hww  4096 May 26 14:42 ./
drwxrwxr-x 4 hww hww  4096 May 26 13:56 ../
-rw-rw-r-- 1 hww hww    20 May 26 14:36 lastsnapshot
drwxrwxr-x 7 hww hww  4096 May 26 14:36 snapshots/
drwxrwxr-x 2 hww hww  4096 May 26 14:23 src/

hww@my-domain:~/workspace/rsyncbug$ cd src
hww@my-domain:~/workspace/rsyncbug/src$ ll
total 20
drwxrwxr-x 2 hww hww 4096 May 26 14:23 ./
drwxrwxr-x 4 hww hww 4096 May 26 14:42 ../
-rw-rw-r-- 1 hww hww   86 May 26 13:59 first
-r--r--r-- 1 hww hww  175 May 26 14:04 second
-rw-rw-r-- 1 hww hww   94 May 26 14:02 third

hww@my-domain:~/workspace/rsyncbug/src$ cat *
This is a non-empty testfile, #1.
Its main purpose is to help reproduce an rsync bug.

This is a non-empty testfile, #2.
This one will have its write permission bit reset,
in order to show that rsync will destroy the permission bits
under certain circumstances.

This is the third non-empty testfile, #3.
Its main purpose is to help reproduce an rsync bug.

hww@my-domain:~/workspace/rsyncbug/src$ cd ../snapshots/
hww@my-domain:~/workspace/rsyncbug/snapshots$ ll
total 8
drwxrwxr-x 2 hww hww 4096 May 26 14:51 ./
drwxrwxr-x 4 hww hww 4096 May 26 14:42 ../
hww@my-domain:~/workspace/rsyncbug/snapshots$

hww@my-domain:~/workspace/rsyncbug/snapshots$ cd ..
hww@my-domain:~/workspace/rsyncbug$ snap=`date  +%F-%H-%M-%S` &&  \
> rsync -ar --itemize-changes src/ snapshots/`echo $snap`/ && \
> echo $snap > lastsnapshot
cd+++++++++ ./
>f+++++++++ first
>f+++++++++ second
>f+++++++++ third
hww@my-domain:~/workspace/rsyncbug$ cat lastsnapshot
2017-05-26-14-54-39
hww@my-domain:~/workspace/rsyncbug$ ll snapshots
total 12
drwxrwxr-x 3 hww hww 4096 May 26 14:54 ./
drwxrwxr-x 4 hww hww 4096 May 26 14:42 ../
drwxrwxr-x 2 hww hww 4096 May 26 14:47 2017-05-26-14-54-39/
hww@my-domain:~/workspace/rsyncbug$ ll snapshots/`cat lastsnapshot`
total 20
drwxrwxr-x 2 hww hww 4096 May 26 14:47 ./
drwxrwxr-x 3 hww hww 4096 May 26 14:54 ../
-rw-rw-r-- 1 hww hww   87 May 26 14:46 first
-r--r--r-- 1 hww hww  176 May 26 14:47 second
-rw-rw-r-- 1 hww hww   95 May 26 14:47 third
hww@my-domain:~/workspace/rsyncbug$

hww@my-domain:~/workspace/rsyncbug$ snap=`date  +%F-%H-%M-%S` &&  \
> rsync -ar --itemize-changes --link-dest=`pwd`/snapshots/`cat lastsnapshot`/ src/ snapshots/`echo $snap`/ && \
> echo $snap > lastsnapshot
hww@my-domain:~/workspace/rsyncbug$

... repeat this a couple of times, then

hww@my-domain:~/workspace/rsyncbug$ cat lastsnapshot
2017-05-26-15-01-35
hww@my-domain:~/workspace/rsyncbug$

hww@my-domain:~/workspace/rsyncbug$ find snapshots/ -name second -ls
1178241    4 -r--r--r--   4 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-18/second
1178241    4 -r--r--r--   4 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-00-53/second
1178241    4 -r--r--r--   4 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-35/second
1178241    4 -r--r--r--   4 hww      hww           176 May 26 14:47 snapshots/2017-05-26-14-54-39/second

hww@my-domain:~/workspace/rsyncbug$ rsync -r --delete `mktemp -d`/ snapshots/2017-05-26-15-00-53/
hww@my-domain:~/workspace/rsyncbug$

hww@my-domain:~/workspace/rsyncbug$ find snapshots/ -name second -ls
1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-18/second
1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-35/second
1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-14-54-39/second
hww@my-domain:~/workspace/rsyncbug$

hww@my-domain:~/workspace/rsyncbug$ snap=`date  +%F-%H-%M-%S` &&
>  rsync -ar --itemize-changes --link-dest=`pwd`/snapshots/`cat lastsnapshot`/ src/ snapshots/`echo $snap`/ &&
> echo $snap > lastsnapshot
cf...p..... second
hww@my-domain:~/workspace/rsyncbug$

hww@my-domain:~/workspace/rsyncbug$ find snapshots/ -name second -ls                                    1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-18/second
1178252    4 -r--r--r--   1 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-18-34/second
1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-15-01-35/second
1178241    4 -rw-r--r--   3 hww      hww           176 May 26 14:47 snapshots/2017-05-26-14-54-39/second
hww@my-domain:~/workspace/rsyncbug$