Thanks, Jellby. What I did was to batch-add the prefix “ch” to the numbered file names (now ch01.html, for example) using Applescript, which is similar to your solution, albeit not as easy! Then I did a search-and-replace in Text Wrangler for the old names in the EPUB files, replaced them with the new ones, and ran the EPUB back through the ePubChecker. The EPUB passed the check and preflight with no warnings or errors.
I like your solution better, so if/when I encounter this situation again, I will definitely follow this.
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