I had some  similar problem
<http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/RollbackBoundry-Can-t-Upgrade-or-uninstall-bundle-td7598888.html>
  
a few weeks back, and while Bob's suggestions were helpful, I set aside that
problem to work on some other fires, and did not return to complete the
analysis.  What did get me past the problem, for the moment was to comment
out all of my uses of <RollbackBoundry />

I believe what was going on was that my bundle chain had several
PackageGroupRefs to ExEPackages which were marked as permanent.  Then I had
a RollbackBoundry.  Then I had various MSIs.  So I think my scenario was
that the MSI after the RollbackBoundry had a problem.  So when I deployed
the new bundle (with all packages and the bundle built with new versions and
product codes), the new bundle caused the old bundle to uninstall.  But the
uninstall exits with success as it seems to think that nothing is installed,
because all msi packages were previously uninstalled on rollback.  The
bundle never uninstalls due to the permanent packages still in the chain
prior to the RollbackBoundry.

Again, this is theory, and unproven at this point.  After removing all of
the RollbackBoundary authoring, and start testing on a clean VM, I did not
duplicate the problem again.  I have not had a chance to get back and focus
on this specific issue.



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