Antonio nails it, I think (except we're talking about copyright, not intellectual property rights). Assuming there aren't any special contractual agreements, the copyright of the photocopies belong to the person who made the photocopies. It would be the same with photos. They belong to the photographer, even if the original manuscript doesn't.
Jonathan raises some interesting special cases, but I am certain your colleague can go ahead and use copies of the photocopies in a publication without any risk of prosecution.
Best,
Dominik
Hi Clemency,
The photographs are the intellectual property of the researcher and can use them as they see fit - unless the terms of sale of the manuscript to the museum contained restraint of use clauses - which may or may not be legally enforceable in an Indian court.
Kind regards,
Antonio
UQ
Australia