Edit : I solved my own problem, you use layers! I hadn’t gotten around to learning those yet and by randomly watching a video about OSC I saw Arminas create an entirely new Root node within the same project and thought, “Hold on, how did he do that?!” and found my answer 
Once I have the different effects running in their own seperate layer I can switch between them with the Solo button and the NDI video output just flips between them with no issue.
I’m sending the video feed from Notch directly to the NDI Studio Monitor which works totally fine and I get the watermarked output as expected. If I open a new project within Notch the video on Studio Monitor gets stuck on the last frame. From the log when running the original loaded project I can see when I hit play :
23:30:50 : Initing NDI Library.
23:30:50 : Initialised NDI Library. Version: NDI SDK WIN64 03:35:12 Mar 25 2020 4.5.0.0
23:30:50 : NDI initialisation done.If I open a new project it doesn’t do NDI initisalisation again when re-enabling NDI output unless I change the name of the NDI Sender and switch between them (thus making the original one essentially dead unless I open a seperate instance of Notch for each one). Is there any way around this other than creating multiple NDI Senders and letting them all be stopped once I eventually close Notch or am I missing something obvious? I’m using the Learning version so maybe something like this is beyond the scope of what it’s meant to be used for!