Can I remove or edit an include() from a function with a filter?

It is not (easily) possible to interfere with PHP include.

What you can do in general is:

  1. Fork a function (create your own copy under different name)
  2. remove_filter() the original function
  3. add_filter() of your function in its place

However that can get impractical very fast.

If the file being loaded makes sense to be customizable the first thing I would do is suggest to plugin developers to make it easily so, introducing a specific filter for it or otherwise.