git merge deletes my changes

Hello Git experts,

A week ago, I've reset a state of 'ceph-ansible' folder in %current% branch with code from corresponding branch (that tracks an upstream from github):

# git read-tree --prefix=ceph-ansible/ -u ceph_ansible

Then I've committed several changes, including:

1. Renamed file and commited:
# git mv site.yml.sample site.yml

2. Made some changes and committed

3. Pulled updates from original branch by:
# git merge -s subtree --squash ceph_ansible

It said:
    Auto-merging ceph-ansible/site.yml.sample
    blablabla
    Squash commit -- not updating HEAD
    Automatic merge went well; stopped before committing as requested

I can see that "my" ceph-ansible/site.yml is deleted (as well as few new files added by me), ceph-ansible/site.yml.sample is restored and doesn't contain my changes (it's just restored to the state before my changes). `git log ceph_ansible site.yml.sample` shows the latest change on ceph_ansible branch done from 26th of August, 2016, my changes in %current% branch was this October, so it shouldn't be any conflict either (even if it was). I believe there is some obvious explanation for this behavior. Could you help me please? What information can I provide in order to troubleshoot this issue?

A post on SO: http://stackoverflow.com/questions/39954265/git-merge-deletes-my-changes

With best regards Eduard Egorov