Given that over the past few revisions of baselayout I have had problems with nonfunctional /etc/init.d scripts, it would be a good idea if as part of the install process baselayout automatically copied the current contents of /etc/init.d to /etc/init.d.old or some other appropriately named directory. That way, if, say, net.eth0 got killed by the new version of baselayout, it would be easier to restore.
Merge the old version again.