Last month Google, Microsoft & Yahoo! Back SiteMaps Protocol, so it makes sense to begin converting your sitemaps to one standardized file. One such webmaster did that, submitted the new file to Yahoo! and claimed that Yahoo!'s Site Explorer dropped half of his pages from the index.
A WebmasterWorld thread has more details;
The day after switching to the new sitemap.org protocol recognised by the big three, our Y! siteexplorer interface showed a 50% reduction in pages listed in Y!
This was confirmed with a site:domain search two days later.
So he switched back and hopes that it will now soon fix itself. Why did it drop by 50%? Well, the webmaster believes; "because he used the identical urls in both sitemap versions, only changing the protocol of the sitemap."
I have no confirmation from Yahoo! on this as of yet.
Forum discussion at WebmasterWorld.