### 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)

PhysicsBody3D(PhysicsServer3D::BODY_MODE_STATIC) {
	joint = PhysicsServer3D::get_singleton()->joint_create();
	reset_physics_simulation_state();
}
PhysicalBone3D::~PhysicalBone3D() {
	if (joint_data) {
		memdelete(joint_data);
	}
	ERR_FAIL_NULL(PhysicsServer3D::get_singleton());
	PhysicsServer3D::get_singleton()->free(joint);
}
void PhysicalBone3D::update_bone_id() {
	if (!parent_skeleton) {
		return;
	}
	const int new_bone_id = parent_skeleton->find_bone(bone_name);
	if (new_bone_id != bone_id) {
		if (-1 != bone_id) {
			// 
			parent_skeleton->unbind_physical_bone_from_bone(bone_id);
		}
		bone_id = new_bone_id;
		parent_skeleton->bind_physical_bone_to_bone(bone_id, this);
		_fix_joint_offset();
		reset_physics_simulation_state();
	}
}
void PhysicalBone3D::update_offset() {