How to avoid errors and what to do if error was appeared, which actions are allowed and which are prohibited, all major recommendations are described below

Recommendations:
1. You must always have at least two scenes: first one with model was prepared to create BonyFace rig (initial scene), second one where BonyFace rig was already created and model was skinned, so BonyFace progress of the model is "skinned" - this is the main scene for animation
2. You have to create .bfs file with splines for every model, spline adjustment is the longest and boring process in whole BonyFace workflow, but after that, when splines were adjusted and saved, you may re-create rig for this model even with changed topology as many times as you want (but for that you must keep initial scene from above post and adjusted splines in .bfs file)
3. During the splines phase save .bfs file every time after partly adjustment: adjust forehead - save splines into .bfs, adjust eyes - re-save .bfs and so on. In this case you can always turn back to previous state with correct splines if some spline controls will be moved in wrong positions during the spline phase by loading just saved .bfs file.
4. Never save the scene with BonyFace splines (during the splines phase), because spline system is driven by callbacks, but callbacks are not saved with the scene and if you load such scene - you can't work with these splines, can't save or continue adjustment, can do nothing. Save splines into .bfs files only and load them every time when you need to create rig.
5. If you have initial scene (before applying BonyFace) and adjusted .bfs file for it then optimal process to create rig is: load scene, run BonyFace, pick objects, load splines, autorig, adjust controls (optional if needed), autoskin. Whole workflow usually takes around 5 minutes including delays during autorig and autoskin phases.

Actions are denied (if you ignore these prohibitions then i absolutely don't guarantee the normal work):
1. Save the scene with splines (during splines phase)
2. Rename or remove any object, layer, controller or modifier if a name of it contains "BF" - it means belonging to a rig
3. Change hierarchy of objects or controllers of the rig
4. Change model topology while working in BonyFace (add or remove modifiers, vertices, polygons). You may change topology before applying BonyFace or after

What you have to do if there was an error (script shows error message or there was a "freeze" during autorig or autoskin phase):
1. If script shows error message or freezes at autorig or autoskin phase, then load initial model, search and fix bad topology (unwelded vertices, unnecessary elements), load splines and repeat autorig and autoskin phases again
2. If script shows error message while working with Extended Tools or in Setup Rig window, then close the window where error was be and re-open it again. To continue something in errored window it is useless