If I understand you correctly, yes, there are two different archives for
the two different Eclipse versions (and yes, reinstalling via update is
a pain):
download.eclipse.org/technology/mylar/update-site/e3.2
download.eclipse.org/technology/mylar/update-site/e3.1
But in earlier 0.4.x versions there was a problem with an Eclipse
version-independent feature (Bugzilla) specifying a 3.2 update site
only, and for some the update manager chose to use that feature to
update the Mylar IDE Integration feature, hence the need to reinstall
for those that saw this.
From now on all updates, whether automatic or not, should work as
expected. Please post if they don't.