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Barty - one way would be to put them into an archive, I suggest a .7z, because calibre can process zips and rars in various ways, whereas it doesn't do any processing of .7z archives - which means you are less likely to get confused.
If you want quick and easy access to the files that are stored elsewhere, you can put a link into a custom column and then click on the link in Book details sidebar.
Or you could do both - keep originals in a .7z in the library for safekeeping, and break out a copy into a scratch location as and when needed,and put a link into a custom column for easy reference.
You'd put the link into a column something like this
I would edit the column in the book list via F2, which will take you to here
Then in the Book details sidebar you'll have something like this to click
BR