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.

Comments:
Andrew
12/05/2006 04:01 pm
A major site of mine (~10,000 visits/day) experienced a 33% drop in Yahoo traffic in the last month. I hadn't yet found the cause, but this sounds like a likely candidate.
Tim
12/05/2006 06:36 pm
This is simply not true. Tim
Jacob
12/06/2006 12:59 pm
I remember people griping about this kind of behavior when Google first launched sitemaps, and I dismissed it. UNTIL I tested using a client's redesigned site, and I saw it happen -- indexing dropped to a fraction of what it should have been. We gave it about two weeks, removed the sitemap, and the site miraculously re-indexed.
John
12/22/2006 10:36 pm
Jacob, did you see the same thing happen with Yahoo's sitemap? I have a client that this happened too as well. As soon as I submitted their sitemap on Yahoo the total # of indexed pages dropped. We actually saw a huge drop from Oct to Nov, and they still haven't gotten back up to "normal".
Jacob
12/28/2006 06:14 pm
John -- I never got to test with Yahoo since the client dropped their interest in SEO fairly quickly.