> I am remembering that make replace seems to not work right when run as a
  > normal user.  That is probably the problem here.

  You are right, running as root fixed it.  Why would that break after
  50-or-so packages?

I have no idea.  Probably it will be become clear when we find the bug.

  Did it start doing something differently after the
  initial ones?

pkg_rolling-replace?  No, it really doesn't do anything different - the
logic is very simple: make the list of dependencies and what needs
rebuilding, tsort, do first one.  Well, it's slighly more complicated to
pick up build-time dependencies, but it is a giant while loop
essentially.

  Is anyone working on fixing it?  (not volunteering, just curious)

I'm not sure anyone is.  I should try - I bet this isn't that hard to
fix.