Zynthian uses an algorithm to automatically connect audio signals, routing mono sources to both inputs of a stereo destination and both legs of stereo sources to mono destinations. This mostly works very well and provides a simple interface with the routing you (usually) require. What is not handled is side-chaining, that is the use of one signal to control a processor processing another signal. In fact, processors with sidechain inputs behave very badly because their sidechain inputs are treated as main audio inputs.
I am working on resolving this but it will almost certainly require manual curation of processor side-chain inputs as I cannot see a way to automatically detect these. To this end, I have searched the plugins for those that mention “side chain” but I am unlikely to have found them all! If you know of plugins that do not work properly due to extra audio inputs or plugins that have sidechain inputs, please report them here so that I can be sure to have captured as many as we can.
This may also affect multichannel plugins - anyone with experience of using such plugins please help to ensure they work the best they can.