I work for a newspaper where I design all of the pages.
I've this problem before and just experienced it today.
I have the A section set up as one document. On one page (A4) I noticed that random elements were gone. Headlines, ads, cutlines. As luck would have it, I had already sent the page to press so I didn't have to remake it. But this is an extreme worry that elements dissappear.
Also, the pasteboard for that spread (pages A4-A5) become extremely large.
Any idea what could be causing this? I have screen shots attached. Please note that the page you're looking at on the left, A4, was completely designed, but at some point elements went missing.