Assuming the submodule's repository does contain a commit you want to use (unlike the commit that is referenced from the current state of the super-project), there are two ways to do it.

The first requires you to already know the commit from the submodule that you want to use. It works from the “inside, out” by directly adjusting the submodule then updating the super-project. The second works from the “outside, in” by finding the super-projects commit that modified the submodule and then resetting the super-project's index to refer to a different submodule commit.

Inside, Out

If you already know which commit you to want the submodule to use, cd to the submodule, check out the commit you want, then git add and git commit it back in the super-project.

Example:

$ git submodule update
fatal: reference is not a tree: e47c0a16d5909d8cb3db47c81896b8b885ae1556
Unable to checkout 'e47c0a16d5909d8cb3db47c81896b8b885ae1556' in submodule path 'sub'

Oops, someone made a super-project commit that refers to an unpublished commit in the submodule sub. Somehow, we already know that we want the submodule to be at commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c. Go there and check it out directly.

Checkout in the Submodule

$ cd sub
$ git checkout 5d5a3ee314476701a20f2c6ec4a53f88d651df6c
Note: moving to '5d5a3ee314476701a20f2c6ec4a53f88d651df6c' which isn't a local branch
If you want to create a new branch from this checkout, you may do so
(now or later) by using -b with the checkout command again. Example:
  git checkout -b <new_branch_name>
HEAD is now at 5d5a3ee... quux
$ cd ..

Since we are checking out a commit, this produces a detached HEAD in the submodule. If you want to make sure that the submodule is using a branch, then use git checkout -b newbranch <commit> to create and checkout a branch at the commit or checkout the branch that you want (e.g. one with the desired commit at the tip).

Update the Super-project

Checkout in the submodule is reflected in the super-project as a change to the working tree. So we need to stage the change in the super-project's index and verify the results.

$ git add sub

Check the Results

$ git submodule update
$ git diff
$ git diff --cached
diff --git c/sub i/sub
index e47c0a1..5d5a3ee 160000
--- c/sub
+++ i/sub
@@ -1 +1 @@
-Subproject commit e47c0a16d5909d8cb3db47c81896b8b885ae1556
+Subproject commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c

The submodule update was silent because the submodule is already at the specified commit. The first diff shows that the index and work tree are the same. The third diff shows that the only staged change is moving the sub submodule to a different commit.

Commit

git commit

This commits the fixed-up submodule entry.