I would explore if you can achieve your "split project" objective working with rather than against the QGIS data paradigm (projects stored separately from layer data).
It sounds like you currently have a single directory
MainProjDir with files (simplified and illustrative):
You're now intending to split into
That is, 2 projects in separate directories, each with its own copy of the layer data. This is doable, but e.g. later changes to roads or footpaths in one project will only affect that project's copy of the data and not propagate to the other.
Why not just create 2 projects in
MainProjDir each using the data it needs:
MainProjDir\HikeA.kml (this one used just by HikeProj)
You can now clear unnecessary layers (and other elements) from each of the 2 projects, while letting them share the same underlying layer data where they need to, and therefore avoid propagation issues.
To do this, you could just save a copy of
HikeProj.qgz and then proceed to edit each project independently. (Just, of course, make sure that you only remove unneeded layers from each project's layer tree, not delete the layer's data files from the browser!) You can also change the styling of each layer in each project independently. But if you edit a layer's data in one project, the data edits will be saved in the underlying layer data files and available in both/all projects.
As an alternative, you could start
HikeProj.qgz as a new project (in the same directory, just with a different project name). Keep it open in QGIS, but then in the Browser window, Project Home tree item, find and open up the Main project and drag and drop desired layers into your new project (drag into the canvas area or the layer tree area). The chosen layers will be brought over together with their formatting from the main project. This is as opposed to adding them from scratch in the new project, when you would have to restyle them.
Finally, if you want to keep your specialized layers (e.g. hikes) for the new project in a different directory, go right ahead. Just make sure to refer to the original layer data files for any shared layers (e.g. base map, roads, ...) in their original location.