Hey Abhijeet,
It is not clear, what you mean by "mirroring each other".
Since you are working on a large model, I would suggest you to use Subsystems by dividing your model. Doing so, you would have a modular design and you would be able to reuse components. Subsystems would also provide abstraction of complex functionalities of the model.
I would also suggest to use model references as it would help in parallel development. It would improve model reusability and it would be easier to have version control for each referenced model.
Both subsytems and model references would help in organizing while creating a hierarchy in model. Do not manually copy paste a section of model, instead export it as a subsytem.
The Simulink also provides a way to compare and merge models. Refer to the following documentation for more information: https://www.mathworks.com/help/simulink/slref/compare-and-merge-simulink-models.html
Please feel free to share any model files and steps to reproduce the issue.
I hope this helps!
