1) The comment count on many articles appears to be zero, even though there are definitely comments. (466 in the one example I was testing). This affects some conditional content on the page (as in "there are no comments on this article yet", followed by ... comments :-). However the next time a comment is added, the correct comment count is calculated.
Is there a way to force all the comment counts to be updated properly? A simple republish of the affected article does not work. I'm shying away from a full site republish. (Large site.)
2) I use .html as an archive path. The dash character used to be stripped out, and now it's treated as a normal character. (Titles like "Something - something else" turn into "something-somethingelse" where in the past they were "somethingsomething_else"). Anyway to get my old behaviour back?
Many thanks,
Leo
Reported on Movable Type 4.2

It might be a good idea to export your blog and reimport it after such a huge jump in MT versions. That said,
with respect to number 2, check this out:
http://www.movabletype.org/documentation/appendices/archive-file-path-specifiers.html
When you open up your templates, you'll see a mapping option. You can specify the path to be the way you want it based on the aforementioned documentation.
On #2, I've spent a fair amount of time on that page. Problem is that I don't see an option to tell it "don't treat a dash as a character". This all seems very reminiscent of bug patched in an old version of MT: http://www.movabletype.com/blog/2005/06/utf8-dirify-bug-and-patch.html
It seems to be a fundamental difference in the behavior of dirify, which is somewhat annoying. (And yes, I've seen the warning that says "don't rely on dirify" that appeared on that pages as well ... in which case - what's the point of having it if its behavior can change without warning?)
I continue to use it because it gives me the FULL title as my archive path, not just the first N characters. Perhaps there's an alternative that would work and strip dashes along the way as 3.2 apparently did?
Leo
OK, set aside the dash issue. I see a long discussion on it over on pronet. My solution found there was to load the http://mt-hacks.com/20080912-dirify-old-restore-the-old-pre42-dirify-function.html plugin and all is well for me.
New problem will be posted to new thread.
Thanks,
Leo