I moved my site, l156.org, from one directory to another before enabling multisite by following both of the relevant codex articles. Everything seems alright on the main site, except that all of the links from the My Sites section give Page not found errors. When I insert the new directory name into the URL, it does find the proper pages. From any of those network admin pages, all of the links include the directory name and work.
I did stick to the codex articles with the following two exceptions:
- Between those two major changes, I did have to change the content links, for which I used Velvet Blues Update URLS.
- I added the
.htaccessrules to both the directory moved to as well as the root before I noticed the discrepancy on the Network Setup page. I have since commented those lines with no change.