When repo2 does the pull, shouldn't there be any comparison between the newly fetched file and the file in the local storage?
A pull happens in two phases: The first phase is just fetching the changes from the remote repository. This is a completely non-destructive action. If anything, it will add unique objects to your repository, expanding the object database. It will also update the remote branches which are essentially branches of the remote you are fetching from.
The second phase is a merge. Git will first check what changes have been made locally. As you didn’t commit anything else, there are no diverging changes and no merge is required. As such, Git can just update your local branch’s history to match the remote’s. At this stage, Git will also attempt to check out the changes so that your working directory will match the just pulled state. In case of a clean working directory, that means that there are no local changes of tracked files, there is no problem: All changes that might have been done before have been committed and won’t get lost. So Git will just update the local branch and check the new files out. In case there are local changes, your working directory is empty. Git will then check which files actually would need to be updated. If it can do that easily, it will do it and keep your changes the way they are. In doubt, it will raise an error that your working directory is not clean and abort everything.
So regardless of what’s the case, you will never lose anything.
