Just stick "for reference only" on there.

But yes, each book has a "barcode" that uniquely identifies it. The thing is, these large library systems have dozens of physical buildings all over the city (a paradox? The larger the city, the more likely it is that everyone can walk to the library) and a specific copy of the book lives in a specific library building.

If you decide that one specific copy is the "reference" copy, then nobody can check it out from their local library branch while people that live everywhere else in the city can check it out from their local library branch! So you are going to need to make the "reference" copy a dynamic thing, which is a lot of effort to solve a problem that in real life is really minor.

Big city libraries (at least in North America - I know Toronto is the same) are amazing, because libraries get better with scale. And perhaps because of their nature, they seem to attract the kind of people that are really good at managing them. I doubt you can find a big city library where the residents think it is a cesspool of corruption. They've got the resources and management to just buy extra copies of books - it's not worth doing anything else.