I have assumed that Precomposed is only referring to the motion menus as MPEG2-BD (i.e. the project default transcode setting); not the timeline videos.
I'm not sure from what you are saying whether you are exporting from AE as MPEG2-BD or dynamic linking from AE and setting the Encore default to MPEG2-BD. And in any event, why would you need to change your timeline assets?