This is a manual operation.
When your project is reaching a numerous number of tables, try to organise the database structure by group of tables, cutting where you find the less FK links. use the diagram for that.
Cook does not handle neither cloning, neither splitting.
So when you have separated in two or more parts, recreate them in the builder in a new project with a pretty similar name. (Actually it can even be the same name)
Then use only unique tables names
Download project
Merge some files such as XML config, manifest, languages, SQL scripts, ...
classes and helpers stays the same.
The syntax is unified, so it is easy for you to recreate the SQL links where you have cutted projects.
Once you have started to do it, it is always the same. It might be long if you have a lot of links to repair.
SECOND OPTION : Delete layouts.
Once you have downloaded MVC files, and maybe forked them, just delete the layouts in the builder. (Keep the table, but delete the layouts)
Do this for the simpliest tables and things that you can recreate easily, and where those files are simple to edit manually if any changes happens.
So. Consider to have a copy of the original files generated, and then just delete those layouts from the builder. Here the clone feature would be a must.
I guess you are advanced user and you gonna do it. I am sooo sorry for that. Cook is not perfect and this workaround is a practice that might loose your time, and cook is not for loosing time. I am very aware of this type of problem.
In one hand, Cook will build for FoF in future (using less PHP memory), in other hand I am gonna introduce N:M in next months (using more instancied memory).
So my advice to you would be to split, or to delete the layouts you have already created.
N:M will be attractive, so reserve some left memory for that.