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I would be quite surprised if the switch from git.cmd to git.exe was the root of the change, since the recursive remove step that is failing is not invoking either of them at the point of failure. It is possible that the results from git.cmd are different enough from those of git.exe that the path is not being executed, but that would be very surprising.
I would guess (just guessing) that the deletion failure is due to Windows having a file busy in the directory and the timing is variable so that sometimes it works and sometimes it doesn't. I've seen cases where Windows virus scanners will have a file locked during a scan and other programs will be unable to delete those files.
If it recurs, you might consider disabling virus scanning in the Jenkins workspace, just to see if that reduces the frequency.