Capture One Catalogue renaming my folders

Hi. So, I've just catalogued all of my work in 9.1 I just imported images [kept them in their original place] by folder so I had a nice filing system in Catalog. It would show the drive that images where on and then the way I archive [by project or commission, year and then specific project and then RAW files or finished images.

All great and I can glance at things easily.

I then updated to 9.1.1 and all the filing just disappeared. It just replaced it with random folders. Am I meant to do anything before I update the Catalog?

Thanks.

Mark