It sounds like you want to create a template that can be used for many products. Depending on the design of your project you could simply put all of the shared components in a single comp, then drag that into a new composition with your product footage. If you want to apply a set of animations designed in the master to layers (products) in another composition you should look into animation presets. I use both strategies all the time.
If you could screen capture the flow chart for your project I might be able to give you some better ideas. Just note (or name) the layers that you'll want to replace.
In the meantime, while drawing out flowcharts and such, with a layer (comp) on your timeline selected, drag the comp you want to replace it with from the project palette onto the timeline while holding down the ALT key. It will replace that comp with the new one, and all effects and animations will remain intact.
Chas that's exactly what I was looking for! Of course, if there is a better way still like duplicate a comp and have all
comps inside duplicate as well that would be awesome.
The animation I am trying to preserve is a super simple opacity transition between two comps. I just don't want to have to do it every time, and I wan the lengths of all of my nested comps to always be the same if possible.