After releasing this quick and dirty recipe, it turned out Brow42 had created something better a long time back. Brow's version of the recipe displays the primary and secondary structures, and lets you change them right in the recipe dialog. This is a lot better than my initial approach, which requires running one recipe to write out the structures, editing the scriptlog file to save the results, and running another recipe to restore the structures.
See "AA Copy Paste Compare v 1.1.1 – Brow42" for a full-function recipe that works with both primary and secondary structure. https://fold.it/portal/recipe/38147
I created "SS Edit" as simpler version of Brow's recipe, that works only with secondary structures in a single dialog box. https://fold.it/portal/recipe/49164