Merges not reporting all changes in relation to parents

Please notice the following merge:

(17 Jun) 69caae9 : https://github.com/mpg-age-bioinformatics/flaski/commit/69caae9bfdb8b62cf76e09553e0710fe5293e542

With parents:

(17 Jun) 97b6d93
+
(16 Jun) 7e70270

In 7e70270 the file flaski/apps/main/david.py got changes eg. Line 123 verbose=False.

This file did not got any changes reported in 97b6d93 nor in the merge 69caae9. Nonetheless, if you look at the file in 69caae9 you will see that the changes from the parent 7e70270 are lost with eg. the value for verbose in 7e70270 is verbose=True.

This is not reported in the merge 69caae9. But once a pull is done by someone on a 7e70270 the following output is given:

laptop:~/flaski$ git pull
remote: Enumerating objects: 16, done.
remote: Counting objects: 100% (16/16), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 16 (delta 14), reused 16 (delta 14), pack-reused 0
Unpacking objects: 100% (16/16), done.
From https://github.com/mpg-age-bioinformatics/flaski
   7e70270..69caae9  master     -> origin/master
Updating 7e70270..69caae9
Fast-forward
 flaski/apps/main/david.py                                     | 158 +++++------------
 flaski/apps/main/histogram.py                                 | 137 ++++++++++++---
 flaski/apps/main/pca.py                                       |   9 +-
 flaski/apps/routes/david.py                                   |  10 +-
 flaski/apps/routes/histogram.py                               |   3 -
 flaski/templates/apps/histogram.html                          | 732 +++++++++++++++++++++++++++++++++++++++++++----------------------------------
 flaski/templates/apps/pca.html                                |   6 -
 utils/notebooks/.ipynb_checkpoints/histogram-checkpoint.ipynb |  61 ++++---
 utils/notebooks/histogram.ipynb                               |  22 +--
 9 files changed, 632 insertions(+), 506 deletions(-)

ie. files like

flaski/apps/main/david.py   
flaski/apps/main/pca.py
flaski/apps/routes/david.py 
flaski/templates/apps/pca.html

are being reported as changed although this is not shown on GitHub neither on 97b6d93 nor in 69caae9.

What do you mean by “not reported”? If you are not seeing changes when looking at the merge commit itself that is normal, the merge commit will contain changes made during the merge, e.g. while resolving conflicts.

Do git diff 97b6d93..69caae9 and git diff 7e70270..69caae9 show the changes you would expect to see relative to each parent commit?

git diff 97b6d93..69caae9 shows me no changes.

git diff 7e70270..69caae9 shows me that 7e70270 was fully overwritten by the content of 97b6d93.

Some of the content in 97b6d93 was newer and it should overwrite 7e70270 but some of the content was older and belonged to the parent of 97b6d93 ie. c6b9c5a which was 3 commits behind 7e70270. Basically this led to the lost of the changes made in 7e70270, 10d9e09, and 7feed96.

Here the history:

69caae9
97b6d93
7e70270
10d9e09
7feed96
c6b9c5a

Was the merge 69caae9 done improperly?

thanks!