Victoria - I have not opened any of the photos in another app since the time they were all displaying correctly so unless the computer pixies did a bit of editing in the night I cannot see how they could have been altered.
I have already made a start rotating the photos as you suggest, but it is such a long task. The rotated images are completely randomly scattered throughout hundreds of folders. I just finished correcting 1,2'' images, total time 45 mins. I have 28,''' images imported so far - you work it out! I just wanted to be sure that they wouldn't all go pear shaped on me again, by trying to understand why.
Anyway, thanks for your help, I think I will just have to put it down to "one of those things" and fingers crossed. Hope you are not snowed in in Southampton like we are here in the Forest of Dean. Or better still hope you are snowed in with lots of food, drink and videos!
Brad - An interesting thought as indeed I had imported some photos as RAW+JPEG (one of the things I like about Lightroom is I no longer need to do this) but when I checked, the rotated images are a mixture of RAW, JPEG and PSD, with only a few RAW+JPEG
Conclusion so far:
Was this pilot error? I cannot for the life of me see how I could have accidentally rotated thousands of images which are in no way connected by any attribute, keyword, folder, metadata etc. But the way LR allows three levels of selection (unselected, selected, and "most selected") and does not follow the normal Windows behaviour of deselecting all other files when you click on one is unfamiliar to Windows users, and it is quite easy to accidentally apply actions to files you thought were not selected but are.