USB Link state is dissconnected while exiting from deepsleep
we should suppose that device end misses its High Speed (HS) 45 ohm
  (namely) termination connection at end of Resume phase.


From the "hardware team" description, your device failed to restore the HS termination after the end of RESUME, which results in HS disconnect (micro-frame amplitude doubles due to absence of termination in your device design).

Please keep in mind that one important part of RESUME protocol is missing in the description: in host-initiated RESUME (K-state), the device must RETURN the SAME line state (K-state) back as a signal of recognition. Host recognizes this two-way driven state when the host-side 20 ms timeout expires, but the bus stays in K-state. Then the host waits for the device to end the K-state, and proceeds with resume of HS idle traffic (SOFs).

So this is the device responsibility to finish the RESUME condition and assert HS termination in timely (1.33us) manner. So it looks like the entire protocol response form your device is missing. Your device receives the RESUME correctly, but fails to respond properly. Some hooks (maybe to power-management part of device software) are missing.