To answer the question of back to v3 - this is not possible. While this was the version in a previous release, it was decided to go back to v2.4 due to compatibility reasons. v3 is not supported.
Indeed, the contents of the .war file is being re-generated upon every build in Worklight Studio. This is true for all previous Worklight versions and not new to 6.1.0. This is the expected behavior.
It is not recommended in any way to edit the web.xml file during development (since it will be over-written). As consequence it is not recommended for production either, because if you do any changes in your project and then re-deploy the .war file, it will not contain your previous post-build changes.
See the comments in this question: Worklight Init Servlet
What you can try, based on the comments, is:
Another option might be to have a separate servlet deployed to your server (not part of the WL .war) and communicate with it using HTTP adapter