As of the Jun 26 12:16:42 2017 (MDT-0600) Nightly Build, the version and directory (folder) structure have changed. You will notice if you download and extract a Nightly Build that the base directory (folder) will be
PhantomBot-126.96.36.199-NB-yyyymmdd. This is to make it clear as to the build being a Nightly based on the folder name, you of course can rename this as you see fit.
Additionally, you will see the version change when launching PhantomBot, and the check for a new release has been disabled as folks running the nightly should be aware that a new version is released almost daily. The new representation of the Nightly Build will look like:
[06-26-2017 @ 18:18:31.794 GMT] PhantomBot Version: 188.8.131.52-NB-20170626