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Upgrading .unitypackage files is a little more difficult.  This quote from the Unity docs explains it:

"For the cleanest possible upgrade, it should be considered to remove the old package contents first, as some scripts, effects or prefabs might have become deprecated or unneeded and Unity packages don't have a way of deleting (unneeded) files (but make sure to have a security copy of the old version available)."

The easiest way I've found is to use the approach the SVN docs recommend for vendor branch upgrades.

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Subscribe to a certain type of message

vhmsg.SubscribeMessage("someMessage");

Subscribe to all vhmsgs

vhmsg.SubscribeMessage("*");

Send a vhmsg

vhmsg.SendVHMsg("someMessage someParam1");

Handle a message

vhmsg.AddMessageEventHandler(new VHMsgBase.MessageEventHandler(VHMsg_MessageEvent));

void VHMsg_MessageEvent(object sender, VHMsgBase.Message message)

{
     string [] splitargs = message.s.Split( " ".ToCharArray() );

     if (splitargs[0] == "someMessage")

          // Do Something

}

Build Process

You can customize the build process by creating and modifying a BuildSettings.xml file.

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