### Godot version

Godot 4 stable and Godot 3.x LTS

### System information

Fedora linux

### Issue description

If you use some custom logic inside _integrate_forces() to alter the state linear velocity and there is any reference to linear_velocity in physics process, the result in godot 3.5 is that it moves just a little bit, while in godot 4 is totally still.

### Steps to reproduce

For the example i created a simple scene in which i apply a force on the linear velocity in  _integrate_forces()  and added a line that add zero to it in physics process. You will not see any move, but it will work fine if you comment the line adding zero.


### Minimal reproduction project

[PhysicsBugReproduction.zip](https://github.com/godotengine/godot/files/12139772/PhysicsBugReproduction.zip)

_reload_joint();
}
#ifdef TOOLS_ENABLED
void PhysicalBone3D::_set_gizmo_move_joint(bool p_move_joint) {
	gizmo_move_joint = p_move_joint;
}
Transform3D PhysicalBone3D::get_global_gizmo_transform() const {
	return gizmo_move_joint ? get_global_transform() * joint_offset : get_global_transform();
}
Transform3D PhysicalBone3D::get_local_gizmo_transform() const {
	return gizmo_move_joint ? get_transform() * joint_offset : get_transform();
}
#endif
const PhysicalBone3D::JointData *PhysicalBone3D::get_joint_data() const {
	return joint_data;
}
Skeleton3D *PhysicalBone3D::find_skeleton_parent() {
	return find_skeleton_parent(this);
}
void PhysicalBone3D::set_joint_type(JointType p_joint_type) {