Thanks guys -- between your comments, and a couple of private e-mails I've received, I now think I can confidently (and properly!) encode to flac. FYI, someone DID point me to what is apparently a brand-new-today FLAC FAQ page at etree. It's interesting and useful, although it suggests that adding tags is a critical part of the new "flac etiquette." I'll see if I can get tags to work using etree's suggestions, but otherwise it sounds like it won't be cataclysmic if they're missing, and all agree flacs (even without tags) are better than un-seekable shns.
Here's the etree-related page:
http://wiki.etree.org/index.php?page=FlacFaq
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