I have made a patch against References.lyx. (posted to -doc) This patch includes a suggestion to use "diff -B -c" to create patches against lyx files. These are the only set of options to diff I found that did not corrupt the whitespace in References.lyx or create hundreds of irrelevant changes due to automatic reformatting of the entire References.lyx file.
However, I would like to check: are these the correct flags we should use for diff-ing .lyx files? -- John C. McCabe-Dansted Masters Student