Peugeot 406 HDI immobiliser problems - dean_ntu

I hope someone can help me.
My brother has a Peugeot 406 hdi that has been stood for a couple of weeks and when he went to start it this weekend the battery was flat.
Having removed the battery and recharged it, the engine immobilser (flip down pad type) now refuses to accept the code...b4 when the code was entered the red light went out and the green light came on and the engine both the green and red lights stay on after the code has been entered and the car refuses to start.
I have checked all of the obvious wiring that is visible and all appears ok...
we have tried disconnecting and reconnecting the battery but still both lights appear and the car still won't start

Any ideas anyone
Peugeot 406 HDI immobiliser problems - ecudecodeing
Peugeot 406 HDI immobiliser problems - Frogeye
HDi with a keypad!!!!!!

Value my car