After upgrading to iTunes 4.7.1 from iTunes 4.7, DRM-protected files that were unprotected with Hymn, refuse to play. However, using JHymn seems a partial solution, as some files still refuse to get copied back to my iPod.

I have found the following page from the Hymn Project:

http://www.hymn-project.org/jhymndoc/

In this page, the reader is instructed to remove the following atoms from unprotected M4A files in order to be playable under iTunes 4.7.1:

(apID)
(cprt)
(iods)

To do so, we will use JHymn. We must instruct JHymn to re-scrub the entire music library, looking for M4A files that were already unprotected, in order to remove any left atoms that trigger iTunes protection countermeasures.