Hi Ravi,
I've Fixed this issue for both the GPIO and LOAN IO.
GPIO
Just make sure when you enable the GPIO's in the peripheral pins in Qsys... that you update the Assignment editor page to include your linked pin
eg.
hps_io_hps_io_gpio_inst_GPIO49 => HPS_GPIO49 -- loans out to the Top level Port HPS_GPIO49 so add this to Assigments > Assignment editor
To [HPS_GPIO49] Assignment Name [I/O Standard] Value [Voltage value of output]
Recompile the project and the GPIO should be available.
LOAN pins are different you need make sure from your Qsys design you export the loanio pins back into your top level design.
hps_0_h2f_loan_io_in : out std_logic_vector(66 downto 0);
hps_0_h2f_loan_io_out : in std_logic_vector(66 downto 0) := (others => '0');
hps_0_h2f_loan_io_oe : in std_logic_vector(66 downto 0) := (others => '0');
the inputs are assigned to the in... and the outputs to outputs... (when they are output make the oe vector for that pin 1 to enable it as an output)
This is pretty much it... happy to help the documentation is brief but pretty much it works well once you do this.
Good Luck
Kyle