The resultant shape should not have BSplineSurfaces. Please verify if that is the case.

The bakeInTransform must be probably removed from there - it will fix the refine but anything after it will be broken as well. It is pretty stupid that it changes the underlying geometry to bspline, I expected it only to move points to new coordinate system and not change geometry types - well, I guess I was wrong.

@Roy-043 good catch, I've verified and everything is BSplineSurface after that:

    >>> for i, face in enumerate(obj.Shape.Faces):
    ...     print(f"Face {i}: {type(face.Surface).__name__}")
    Face 0: BSplineSurface
    Face 1: BSplineSurface
    ...

As discussed with @kadet1090 I reverted that line and commit. Result is that we have normal surfaces:

>>> obj = FreeCAD.ActiveDocument.Boolean
>>> for i, face in enumerate(obj.Shape.Faces):
...     print(f"Face {i}: {type(face.Surface).__name__}")
... 
Face 0: Plane
Face 1: Cylinder
Face 2: Plane
Face 3: Plane
Face 4: Plane
Face 5: Plane
Face 6: Plane
Face 7: Plane

Let's merge that and re-open #25578

The other way to reset the placement is to put the shape in a compound.

The other way to reset the placement is to put the shape in a compound.

IIRC the problem was because the object is in compound and then solids are extracted as subshapes from it loosing the transform (or regaining it?) in the process. I did output the transform for each internal shape and my conclusion was that one of them is simply not accounted for by boolean operation. I have not tried to put it in yet another compound thought, and I'll try to do that - so thanks for suggestion.

Successfully created backport PR for releases/FreeCAD-1-1:

• [Backport releases/FreeCAD-1-1] PartDesign: Fix refine not working with Boolean operations #26762