Nicolas, if you choose to split the project into different parts, then you will have to make sure audio is separated into individual pieces properly as well.
Anyways, I would suggest to divide the topic into more parts, just to have more convenient workflow, and not a single massive .aep project.
Later, you would render out individual pieces and connect them together, either in Premiere if its simple sequence merge, or with AE (if some more complex transition work would be required between the pieces).
To begin with, I would do the following:
1. Create a master project, which has the structure which you are familiar with (including all folders/main comps/repetitive items which might be used later (if possible to plan this),etc)
2. Inside the master, pre-comp audio file.
3. Create ‘part comps’ of the master’s audio file. Each scene will have its own audio layer cut, from master pre-comp (N overall).
4. Save as this project N times with incremental file names and then work on every individual piece animation in each .aep file.
It is as straightforward as it sounds. Based on this you can see, that it is possible to face an issue where the same assets re-use is required for other portion, yet you might not have them in the same project file ☺ There are tools which allows to simplify this, but you can always import other project into panel and leave out only whats needed.
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