Did something that worked for me. YMMV
moved all the emails that the iphone could not download to a test subfolder in yahoo (using a web interface)
then moved them back, one at a time, to the inbox, checking that iphone mail app can see the moves.
by the time I hit the last email, yahoo was having issues opening that one on the server.
Tried that because I noticed that sending using the iphone mail app was working fine, and it seemed to want to download, but was choking on something. in this case, the last email was preventing the rest from downloading.
if we assume yahoo servers had a hiccup around that same date (sept 12) and a lot of users had at least one "clog" email, then that would exlpain the collective odd behaviour.
or I may just have caught a lucky break.
give it a shot.