Andylew - 7:18 pm on Jul 18, 2010 (gmt 0)
Supplementary index for sure, I think this is also tied into mayday. Either the supplementary index is being used as a test bed for caffine before going live or the mayday update was in fact a tweak to the minimum link juice a page requires before it is in the main index. It is likely your pages have gone to the supplemental index for reevaluation and will be added back to the main index shortly.
WebmasterWorld has around a million pages in this supplementery index, it is easy to 'probe' site:domain.com will return main index pages. site:domain.com -lasdkjf (or any spelling mistake) will confuse google so it looks in the supplementary index and will return total pages it has for you. A simple trick but seems to be accurate.
I think what happened with mayday is the the minimum required link juice to enter into the main index was tweaked upwards, therfor the need for deeplinking to create link juice further down into the body of a site has increased substantially the link juice ripples are not strong enough from the home page. It also means for larger sites with lots of pages the link juice is getting spread so thin amongst lots of pages these are now below the main index threshold.