What happens if at the top of the book it says "If you're looking for the awesome HP fan fiction "Methods of Rationality", go HERE"? (Ditto on HPMoR chapters?) Sounds like you might get some free cross-advertising that way, as well as a common brand across products.
Assuming, of course, that you want the common branding.
Another alternative: HPMOR could be renamed. The early chapters might have been explicit in the methods of rationality, cognitive biases, etc., but it has since then developed into a full-fledged story, and only tangentially related to rationality by way of certain characters. (Or maybe that's just me?)
Quantum Computing Since Democritus got me thinking that we may want a more riveting title for The Sequences, 2006-2009 ebook we're preparing for release (like the FtIE ebook). Maybe it could be something like [Really Catchy Title]: The Less Wrong Sequences, 2006-2009.
The reason for "2006–2009" is that Highly Advanced Epistemology 101 for Beginners will be its own ebook, and future Yudkowskian LW sequences (if there are any) won't be included either.
Example options: