Spent far too long trying to troubleshoot a new App Shortcut for Messages with commands like defaults find NSUserKeyEquivalents and mucking about with files such as com.apple.MobileSMS and .GlobalPreferences.plist before stumbling onto App Keyboard Shortcuts Don't Work in Sonoma. Newly-added App Shortcuts in Sonoma do not work for Messages.app; other tested apps (Calendar, Contacts, Dictionary) appear unaffected.
As jamesfromhaymarket points out, one workaround is to set the desired keyboard shortcut for All Applications instead of just Messages; assigning "Delete Conversation…" (press Opt+; for the ellipsis) to Cmd+D this way was successful.
/mac | Jun 23, 2024