I had totally forgotten I asked this already but looking back, no-one actually answered the question, although I must admit I should have replied to the question asked of me in this original post.
In any case the issue is still there.
How do I clear the download history without deleting the file that was downloaded?
Yep known issue and discussed a few times on these forums.
Deleting entry in download history will delete file, sometimes if you move a file to a new directory it will remove the entry from the download log. If the file remains in download log after being moved… Deleting from download log WILL delete file from device