If something like that would happen it would be a very weird bug. No, it isn't supposed to be changed like that, but I believe you can change it even from web UI, on the json configuration page.
But I've already compared the value it complains about in logs you provided to the value that is in your schema files output before, they are the same. As you can see, it doesn't even comes to Gluu, your tomcat is stopped, you start opendj and you get schema error right away. So it comes down to OpenDJ. My guess that if you'll remove all these `edu*` attributes from this custom class's definition it will at least start without problems, but the fact these attributes are mentioned in it means you activated them in web UI and probably using them in TRs and mapping them with CR. So it will again result in schema violation errors, but now because `edu*` attributes are not allowed in user entries.
Okay, here is a dirty hack to try:
1. Stop tomcat and opendj
2. Move the file where the problematic class is defined out of `schema/`
3. Copy just this class definition to the end of the `96-eduperson.ldif` file. I mean only this part: `( ox-09B5355EB99F4FF900017FE54E6A-oid NAME 'ox-09B5355EB99F4FF900017FE54E6A' SUP top STRUCTURAL MUST objectClass MAY ( eduPersonAffiliation $ eduPersonEntitlement $ eduPersonPrincipalName $ eduPersonScopedAffiliation ) X-ORIGIN 'gluu' )`
4. Start opendj
At least this should work. Before starting tomcat again you'll need to restore everything back and restart opendj again. That's just to verify the assumption.