### 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)

if ("linear_limit_enabled" == var_name) {
		axis_data[axis].linear_limit_enabled = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(j, axis, PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_LINEAR_LIMIT, axis_data[axis].linear_limit_enabled);
		}
	} else if ("linear_limit_upper" == var_name) {
		axis_data[axis].linear_limit_upper = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(j, axis, PhysicsServer3D::G6DOF_JOINT_LINEAR_UPPER_LIMIT, axis_data[axis].linear_limit_upper);
		}
	} else if ("linear_limit_lower" == var_name) {
		axis_data[axis].linear_limit_lower = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(j, axis, PhysicsServer3D::G6DOF_JOINT_LINEAR_LOWER_LIMIT, axis_data[axis].linear_limit_lower);
		}
	} else if ("linear_limit_softness" == var_name) {
		axis_data[axis].linear_limit_softness = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(j, axis, PhysicsServer3D::G6DOF_JOINT_LINEAR_LIMIT_SOFTNESS, axis_data[axis].linear_limit_softness);
		}
	} else if ("linear_spring_enabled" == var_name) {
		axis_data[axis].linear_spring_enabled = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_flag(j, axis, PhysicsServer3D::G6DOF_JOINT_FLAG_ENABLE_LINEAR_SPRING, axis_data[axis].linear_spring_enabled);
		}
	} else if ("linear_spring_stiffness" == var_name) {
		axis_data[axis].linear_spring_stiffness = p_value;
		if (is_valid_6dof) {
			PhysicsServer3D::get_singleton()->generic_6dof_joint_set_param(j, axis, PhysicsServer3D::G6DOF_JOINT_LINEAR_SPRING_STIFFNESS, axis_data[axis].linear_spring_stiffness);
		}