site:war creates incomplete war with many files missing

Problem first appeared when upgraded to 1.7. Downgrading to 1.6.1 caused the problem to go away. Now, a month or two later, 1.6.1 exhibits the problem too. Perhaps because the size of our codebase continues to grow it now shows in 1.6.1.

How we create the war:
1) clean all
2) run site on each component
3) run multiproject on the parent to get the dashboard report, its html pages generated, and all subprojects copied into place
4) run site:war to create the war

The war is missing files, including files in the root that are part of the parent (e.g. FAQs) and most content of some subprojects. Yes, these files exist in the target dir.

Interestingly, the -X output shows one of the missing files identified as needed and added on a site:war run that doesn't delete the war first:
[war] [VERBOSE] perforcefaq.html added as perforcefaq.html is outdated.
....
[war] [VERBOSE] adding entry perforcefaq.html

Yet the resulting war does not have that file (and others). Hmm, perhaps this suggests a problem somewhere else...

The site and war is large, runs about 10 hours to generate and the war as-is is around 360M.

I moved the site deploy process to the war approach from the file copy approach, as it was cleaner and a bit faster. I think the workaround is to go back to the file copy deploy approach.