At the time, Eudora would do POP3 by first asking for the message list, then downloading all the messages, then deleting all the messages. If something broke before it finished deleting stuff from the server, there wasn't anything there to check what had already been downloaded so with thousands of copies of a large attachment clogging things up, that was problematic. Fortunately, LIST reports message size and the malware was all in a small range so I could just selectively DELE those.
It was enough messages that it was faster to write a program to do it than to telnet to the mail server and run the commands manually (which I started with as proof of concept).