Have you checked the layers and sublayers of the affected pages to make sure that nothing has been turned off accidentally? Have you also checked all of that for any adjustment of transparency that might have occurred? It is possible that the document has somehow corrupted. If that is the case then there are a number of places on the net that specialize in document recovery and repair but I would like to suggest that you try an old method that can sometimes remove corruption and/or artifacts from affected pages. It involves dragging from the Pages Panel of one document to a new document created to the same size as the first. I would try doing this as a test with just the nine pages in question to see if it helps. Position the old document over the new document (which is set to the same page size) so that you can see both documents and select the pages you want to move in the Pages Panel and dragging from the Panel itself onto the pasteboard of the new document below. You will be asked where in the document you want the pages placed and when you click OK the pages from the old will become a part of the new document.
I've had this work in the past. It seems to be more effective than using the Move Pages Option in the Pages Panel but I offer no guarantees. Good luck!
If it does work and you then bring the rest of the pages over you can create new Master Pages using the document pages and the Save as Master option which is found in the Pages Panel pull-down menu under the Master Pages entry.
Thanks for taking the time to reply. All the layers are visible an no transparency issues. It's almost looks like Illustrator when you delete an artboard and the artwork remains. Very strange.
I managed to just insert nine additional pages - and copy and paste the content in place and the document is working fine. Luckily a quick fix this time but I have never seen this happen!