Strategy to integrate 2 web project

My web project look like this,

   +--|--/web project A
      |--/web project B
      |--/library C
      |--/library D

Web project A and B is now integrated into 1 runtime (1 war).
Currently this is done by making all source and resource folder of web project B part of web project A; web project B no longer exist.
However this pose a problem with Eclipse project. The Eclipse plugin generated 1 single eclipse-wtp project which A and B source code inside, while in reality web-project A and web-project B served by different SVN branch.
I want Eclipse project to reflect the SVN layout rather than resulting war layout, which would be 2 eclipse-wtp, 1 each for web project A and web project B.

What is the best strategy to achieve this?

Currently what I have in mind is to create separate sub-project for each web-project. In web-project B, I would override war and build task to do nothing. In web-project A, I would import war definition of web-project B only on build task.
Does this makes sense at all?