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git difftool directory diff problem copying changes back is not reliable

I have a problem with directory diff. The following command:

Git difftool -d _commit_sha_

Opens my compare tool (Beyondcompare) and I can make a folder diff. The tool
also allows browsing through all changes and looking/editing single files (a
beyondcompare feature).
So my workflow would be to open single files and make changes to the right
side of the diff.

After saving and exiting the diff tool sometimes these changes are copied
back to my working tree.
I currently assume from my tests that changes are copied to the working tree
if they are not too deeply nested in folders. So changes to files in folders
up to a depth of about 4 or so are copied back. If any deeper they are not.

My system specs:
OS: Windows 10
Git: 2.19.2.windows.1

Folder of repo. Folder name length is identical to real folder name length
in case it is a folder name length issue: 

Folder for comparison (temp names are really used names):
Commit sha side:
Working tree copy side:

Can anyone confirm this?