I finally figured out the problem, and in fact, it was a little of both. When the server melted down, and our folders were restored, the backup was from a time before I upgraded to MT3.1. As a result, the MT2.6 installation that I had wiped from my account was back. I've kept a few of the older achived entries, so as not to 404 other peoples' links to them, and so, when the comment spammers hit, their comments were triggering 2.6 rebuilds of the entries and the indexes. And all of my 3.1 files that shared filenames were being overwritten as a result. I wasn't losing data, but my index pages and style sheets were being "restored" to their 2.6 versions.
The solution? Re-delete MT2.6, and go through the old archive pages, removing the comment forms. Now the spammers have to get through my active Blacklist installation, and even if they do, the rebuilds will come from 3.1.
(It makes sense to me, even if it's painfully obvious to some, and cryptic to others. I'm happy.)
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