Hi,
I did several migration tests and I am quite sure now that admin/replace.php must be broken. I had installed moodle in a subdirectory like this:
https://dev.example.com/moodle/
and after migrating to a new subdirectory moodle-test I got these kind of broken links all over the sqldump (one example follows):
https://dev.example.com/moodle-test/moodle/moodle/course/view.php.
in the admin/replace tool I just tried to replace
https://dev.example.com/moodle/
with
https://dev.example.com/moodle-test/
what does not seem to work very well.. if the tool is not programmed to replace sites in subdirectories it should warn users about this fact.
If I did anything wrong I am not aware of it, I tried it several times and this behaviour is reproducable.
If anybody with write-access to the wiki is reading, please warn people on pages like http://docs.moodle.org/20/en/Moodle_migration about the immature status of the replace.php tool that is mentioned there, I think tthat would be only fair and possibly avoid lots of problems for a few people who are relying on that tool.
Thank you very much for your attention,
Bughunter