I think the best option available to you is to keep a .hgrc snippet in place in the parent repository filled with [subpaths]
entries. For example create subpaths.hgrc
as a tracked file in your repository:
[subpaths]
repoa = http://remote/path/to/repo/a
repob = http://remote/path/to/repo/b
Then when you want to initialize those repositories you add this line to your clone's .hg/hgrc
:
%include ../subpaths.hgrc
and then comment it out when you want the repoa and repob paths being their usual, local selves.