Git Rebase - Missing merge requests on reboot using master

Question

When reinstalling with the wizard, merge commits disappear, while the code change remains intact.

The state of the initial branch (non-leading) before rebooting:

commit 52c********************************
Merge: 1******
Author: M*********************************
Date:   Tue Feb 9 17:49:25 2016 +0530

    Merge pull request #1342 from *********************

    Changes for ******************

commit 6be**********************************
Author: Ma***********************************
Date:   Tue Feb 9 14:39:48 2016 +0530

    Changes for W********************************
    commit ef2***********************************

Once we reinstall the wizard, there is no compilation in the git log starting with "52c ..".