Git VCS root deletes .git folder

We are using TeamCity Enterprise 2017.2.2 and when I was triggering a build today on one of the .net project (It was working fine before we upgraded to this version), and running the following metarunner:

git fetch origin --tags gitversion /nofetch /output buildserver /UpdateAssemblyInfo

throws me an error:

Not a git repository (or any of the parent directories): .git

When I look at the workdir, it has all the files and folders except .git folder. So looks like, Git vcs root worked initially fine to bring down contents of my project and then it deleted .git folder. Can someone please suggest how can I fix that?