OK, sorted out this problem:
This document uses files in multiple locations that RapidWeaver is unable to access
Two of my four websites gave the multiple location warning on load. I chased this down by duplicating my project and then using the copy deleted a page at a time until the error went away on reloading. Both projects I ended up deleting EVERY page (adding a dummy blank page so I could actually see the project) and still I was getting the warning on load.
I checked the Resources and saw on one project that one of the two resources was showing a cross as ‘unlinked’. Tried relinking this by right-clicking and locating the image file in the folder on the Mac. Saved and reloaded the project, same warning message. Deleted the resource and dragging the image into resources, saved and reloaded - the warning message has gone, problem solved.
The other project was a bit more difficult. Deleted EVERY page (adding a new blank page) deleted the resources, web logo and the web icon images, in fact EVERYTHING in the project except for the one blank page. Still got the warning after saving and reloading.
Created a new 8.1 RW project and dragged and dropped every page from the old project into the new. Added web icon images and site logo and updated the General setting and publishing details. Saved and reloaded the new project - all good, no multiple location warning.