Submodules: git status vs git checkout - untracked files

Question

I have a GitHub fork which is cloned on my laptop.

I also have PR which I am trying to fix.

So what I did is:

git checkout master
git pull
git checkout <my_pr_branch>

At this point I got a failure due to a bunch of unmerged files in one of the Git submodules that was updated in the meantime.

But if I after that do git status - I will not see the untracked files.

Now at this point I could remove those files from my local repo and update the branch. But I prefer to keep my master in sync.

How do I properly update the master and then switch to my PR branch?