YukiMessenger 1.1.0 brings some major updates to how things work - especially in subscribing to messages. Update 1.1.0 also enables the ability for the server (the proxy instance) to receive responses on requests sent to clients (Spigot instances).
Note that this new version of YukiMessenger requires YukiCommons versions 1.0.0 (equivalent to 1.0) or up. This can be found at https://github.com/KuromeSama6/YukiCommons/releases/tag/1.0.0. Again, this plugin works both on Bungeecord and Spigot.
In terms of backwards compatibility, it is advised that developers switch to use the new system if they choose to upgrade from YukiMessenger 1.0.0 to 1.1.0, in order to avoid unexpected behavior that has not been tested.
Check the Wiki for documentation on the new features, as well as the changelog for this update.