Serialised data breaks when using the migration approach documented by http://docs.moodle.org/en/Moodle_migration
Either using /admin/replace.php or `sed` causes the issue.
The severity of the issue depends on what string you are replacing. In PHP 5.1.6, if you edit serialised data and replace a string with one of different length without updating the s:<number>: value to the new length, it will throw a warning and return false. In PHP 5.2.10 it put up with the incorrect length and worked anyway.
If the problem is effecting the course.modinfo field you can simply update mdl_course set modinfo='' to fix. The issue effected a third party block I was using (course_menu block) which used serialised data and contained a URL which I was replacing, causing the block to crash out and not display.
I checked all core code for other uses of unserialise. There are some serialised fields stored in mnet as well as gradebook preferences which could break if they get tampered with.