I have seen this issue twice now and in both cases was assembly involved.
The real problem is not the ShapeBinder, that is in fact shown in the right place, the problem is the clone or an element in the Part container. I have simplified the file a bit further, so that the Part contains only 2 objects. If I delete "GT2 Pulley 20 Teeth" the MotorBracket all of a sudden pops to the position where the ShapeBinder is. The ShapeBinder seems to stay in place only because it is broken due to the now missing face:

- beforeDelete.png (11.84 KiB) Viewed 461 times
and afterwards and performing a recompute:

- afterDelete.png (11.3 KiB) Viewed 461 times
The FreeCAD file attached is the state before delete.