.swf files contain links to .flv files and .xml files which in turn contain links to images, data, etc. The .flv and .xml files are not downloaded and not parsed although included in the project properties.
For example see http://www.deecaffari.co.uk/en/about_dee.html
This means we would have to browse the whole site to find any missing links - for 1,000+ sites, this is a tall order. Could such things be logged so at least we'd know where to look for problems.
If downloaded with autosave - will they be updated when the site is refreshed.
I am sorry that it requires a lot of manual work. But at least it is some kind of solution.