Yeah, I’ve always done this too.
The problem with using long scale strings on a shorter scale is it often means the tapered part at the end, which normally goes round the tuner, isn’t where it should be, so you end up wrapping the full thickness of the string round the tuner, which makes it a bit clumsy. Of course this differs from manufacturer to manufacturer.
I’ve actually found some Warwick black nylon wound medium scale 40-100 online but only available from Europe; can’t seem to find them here, and shipping was about £9, which is a pain. Dunlop also do some medium scale 40-100 flat wound, but they’re £45, which is a bit steep if they don’t work or I don’t like ‘em.