This shouldn't be a big issue since both implementations do nothing more than clear caches, but ...
In 99dfcc3 there's a change to the content of a hook_update_N() function. Since the earlier version of that function was introduced in 2015, we can't change it now and be confident of the outcome. (Again: it's just a cache clear, but we need to make sure it actually runs.)
The git log and issue queue don't show any reason that changing civicrm_entity_update_7200() was required, so I'm hoping this can be resolved by committing a change which restores the older version and moves the changed version to civicrm_entity_update_7201(). That way, people who downloaded 7.x-2.x between last May and today will still have that update applied, as is intended. (If user installed CiviCRM Entity 7.x-2.x in December from Github, and I upgrade to the current beta3, my read is that they will not get an update run and the cache clear won't fire.)
See docs on hook_update_N.
AFAIK, an empty hook_update_N() delivers the desired drupal_flush_all_caches() when update_finished() is called. Adding drupal_flush_all_caches() to a hook_update_N() should then have the caches to get cleared twice - which may be your intent based on previous discussions, so I'll leave 7201() doing that.
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