I’m in the same situation: After having moved to a new server, 90% of the links (and 100% of the images and CSS) on my Moodle installation aren’t working anymore.
I did enable slash arguments, I did delete cache (via the admin login interface), I did run replace.php (as mentioned), and the Moodle config.php configuration is correctly set. Also, I did NOT upgrade the Moodle version, I simply switched servers. I did enable (presumably) appropriate permissions on the Moodledata folder, and of course the Moodle folder itself.
One thing I noticed however, the replace.php function doesn’t seem to be replacing anything, or at least, it’s not replacing what I want it to. I know this because after successfully running the command at the command line, when I check the database references to the old URL are still there, unaffected. At this point I’m not even sure if those DB entries are even the culprit, there are only 5 total entries that list the old URL.
So my main question is, what can I do to get my URLS (and thus images and css) to work?
My secondary question is, are most Moodle URLs/links being generated from information stored in the DB or from the Moodle Data folder? If they are coming from the few references I see in the DB, could I perhaps manually insert/replace corrected entries into the DB?
Thanks for any help!