title: Git is losing history/contents on individual files
body: <p>I work in a small company and our Git repo is a little messed up.  I just did a <code>git pull</code> and my changes made earlier today are gone!</p>
  
  <p>When I work on HEAD on the master branch, <code>git log</code> shows my last commit <em>b94940c63ef965ce45b0d64ccfba4359134d2552</em> in its history.</p>
  
  <p>Now if I do <code>git log filename</code> for the problematic file that lost my changes, that commit is not shown (only shows an earlier commit).</p>
  
  <p>Performing <code>git log --follow filename</code>, my commit <em>b94940c63ef965ce45b0d64ccfba4359134d2552</em> is shown as most recent.</p>
  
  <p>And sure enough if I do:</p>
  
  <pre><code>git checkout b94940c63ef965ce45b0d64ccfba4359134d2552
  git log filename
  </code></pre>
  
  <p>then the commit is shown <em>and</em> my changes are in the file!</p>
  
  <p>In other words, the commit I made is shown in the branch history (blocking a branch merge), but individual modified files do not have that commit in their history!  (unless I explicitly checkout that commit).</p>
  
  <p>Questions:</p>
  
  <ol>
  <li><p>How on earth did this happen?</p></li>
  <li><p>How do I fix it? (We have problems with multiple files in our repo)</p></li>
  </ol>