To checkout files with .git folder; "VCS Checkout mode" should be "Always checkout on client". That is ok but when i need to checkout from another vcs root in the same project, "checkout rules" are not supported. So, second checkout write on previous .git folder.
VCS checkout mode is project specific, not specific to VCS root so, this problem happens. Also "checkout rules" not supported when "Always checkout on client" is selected.
Note: Teamcity version is 2018.2