<p>I voted to close as "Unclear what you're asking" because I genuinely could not follow the question. The main statement of the problem is: </p>

<blockquote>
  <p>My big question is how do I handle one test feature where part of it
  has not been trained?</p>
</blockquote>

<p>...which I didn't really understand till I read your answer just now. And an apparent secondary problem was:</p>

<blockquote>
  <p>The issue that I am running into is the training set has seen the
  ChildPath "C:\Windows\System" and the ChildExe "cmd.exe" which are
  normal, but the training set has not seen the ParentPath
  "C:\Windows\Malicous" or ParentExe "badscipt.exe" so these have not
  been label or one hot encoded.</p>
</blockquote>

<p>...which seems like more of a programming issue.</p>

<p>I notice that your answer also begins:</p>

<blockquote>
  <p>The challenge that you've discovered is a natural consequence of how
  you've organized your research project: your model has no
  generalizable information about new file paths or new names of .exe
  files.</p>
</blockquote>

<p>This also seems to suggest a programming/organisational problem rather than a statistical/machine learning one.</p>

<p>That said, I don't have much expertise in this. So my confidence in my judgement is not very high and I'm willing to reverse it. I do think the question is poorly written, though, and would benefit from some editing.</p>
