 <p>First, find the hash you want to your submodule to reference. then run</p> <pre><code>~/supery/subby $ git co hashpointerhere ~/supery/subby $ cd ../ ~/supery $ git add subby ~/supery $ git commit -m 'updated subby reference' </code></pre> <p>that has worked for me to get my submodule to the correct hash reference and continue on with my work without getting any further conflicts.</p>