Just a thought--not a bug. lilypond-book refuses to overwrite a main source file, but happily overwrites secondary source files included into the main source file. Irritating if you use the .tex extension for included chapters of a musicological document and even just accidentally call lilypond-book without specifying a separate output dir.
"Don't do that." and "Version control!" would be perfectly good responses, and I probably have a few other minor (shrug-worth?) points if there is interest in hearing them. In any case, I'm hugely fond of LP. Truly, thank you, devs and other contributors! - Cam