This is something i have been wanting for a long time (and Unity are actively working on it now) for the purpose of making modular maps where by "sections" can be swapped,moved,rotated etc at run time and the nav-meshes can the merge correctly.
Unity is working on a similar feature where by a nav-mesh for a given prefab can be stored for said prefab and then merged together.
They seem to be "connecting" nav-meshes together using something called a " NavMesh Portal ", no idea how it works... it probably won't be until unity 6.
I will be watching closely how this turns out as it fits perfectly for my needs.
Given unity are working towards this, would you consider it as well after seeing how they approach it, or perhaps you already have an idea of how to do it and would consider it ?