OK, I've spent a few hours upgrading from 2.2.2. First I set up a subdomain at dev.borderlinecollective.org. Did a new install of WordPress, then imported the old site. Made sure it was fine, then upgraded the main domain at borderlinecollective.org. (These are on two separate databases). For the subdomain I did a completely clean install, for the main domain I left the wp-content folder intact (since the dev subdomain was still linking to images on the main domain).
The main site looks fine, but somehow the index page of the dev site has now disappeared...when you go to the link there's an error message. The index page in this particular theme (Andreas Viklund 01-12, very old) isn't a separately-created homepage, it's just the main index template in the theme editor...a blurb on top and then the posts on the bottom (which you can see on the main site). The info in the editor view has not changed, it's still there. All "previous" links are supposed to look the same, the blurb on top is always above the posts. On the dev site you now cannot access any of the archives that way, but all individual posts, or monthly archives or category archives are fine.
When I use my FTP client I see that index.php is still there in the dev folder. The page actually disappeared sometime during the upgrade of the main folder, which led me to suspect it was somehow reading the index page from the main domain. But now that the main site's index is working again, the index for the dev subdomain is still gone.
Any thoughts? My goal was to work on the site's redesign on the subdomain, but I want to make sure everything is working and matching the original site before I do so. And it was definitely there before I started the upgrade on the main domain!