Texture Atlas and island pin functionality

Hello,
I've been trying to use such a workflow:

1. add objects to atlas,
2. start manual unwrapping,
3. go into edit mode,
4. select all,
5. U unwrap,
6. fix some islands and pin them,
7. finish manual unwrapping.

Now when I com back to step 1 and want to again unwrap and keep my pinned islands they are all gone. Is there a way to keep them somehow with Texture Atlas? Or maybe my workflow makes no sense.

Thank you,
Jacek