by Colin Fraser.
Daniel, be careful when reading and reviving a discussion that is so old, the conditions that led to the original error may no longer apply in your version of Moodle. It is perhaps better to start a new discussion but with a reference to the older one. That said...
There has to be some anomaly in the second course causing an error. Is one user enrolled twice? Has someone tried to upload something that does not fit in with the demands of the course, like an unusual file type, not encountered before? Has one file been uploaded that is really large? Is a file corrupted? Lots of issues.
When I have had a backup issue, I go back and take a lot of backups, eliminating that which works, narrowing down to what doesn't. The first being with no user data, and if the error is found, then make a second backup, the top half of the course, if no error, the bottom half of the course, if an error, then one section at a time. More often than not, the error is in the user data, and that is a lot more difficult. Check enrollments, check user uploads, and if nothing stands out, repeat the process with a backup of user data only. If an error occurs there, then I start looking in the database itself, starting with Users.
This is time consuming, and can be frustrating, and does not always yield a positive result. This can result in me sending the entire course, complete with user data into an archive area that is only accessible by Admins, if the User data is important, or deleting the course entirely, replacing it with an earlier backup. As long as there is a record of the results, usually in a separate spreadsheet, that is deemed sufficient as to remain a "viable record" for the results of that course.