Running this in the main repository should do the trick:
git pull --recurse-submodules
According to the other discussion, especially as @Tobu pointed out in his comment over there, if the error persists, it might be needed to first:
remove both the submodule worktree (ext/blah) and the matching folder inside the GIT_DIR (
.git/modules/ext/blah)
Alternatively, you could git checkout the branch from which you want to pull while inside the submodule, and then run a git pull.
Results should be the same.