Ouch. That is weird. Perhaps there's something historical going on where they used to let Harvard students keep their own copyright but a few decades ago changed it to demand copyright, which is why they can't scan the entirety of an old thesis like Todd's. Hm. You could try replying and asking why they can't scan a Harvard thesis given your personal experience.
If that doesn't work and the other guy can't help, I wonder what I could do. Leaving that thesis out is a really big gap in the literature... Going to Harvard physically with a scanner is not an option since I don't know if they would even lend it out of the stacks to me, much less when I'll ever be in Boston again. In an instance of rather bad timing on my part, it turns out Todd died just last year so I can't simply email him and ask him to release it under CC-BY-SA or something and then the Harvard people could be told they have copyright clearance; his wife Joyce is still around, though, so I could try asking her to license the thesis.
Perhaps you could ask the scanners what they would accept as adequate proof of copyright safety, such as some sort of document signed by Joyce? (No point in bothering her if it wouldn't get them to unlock the thesis, after all.)
In my experience, the actual reason is probably not copyright, as was suggested. The ILL software likely has a few canned responses, and "this is too big, we don't want to scan it" likely rounds to the reason received. I've also had a librarian refuse to scan a relatively short document for "copyright" reasons, despite the document being in the public domain, though not obviously so.
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