For anyone having the same problem.

I have found a solution. It seems like it was a battery problem.

What I have done is:

I have connected the N900 battery in parallel with an other cellphone battery by connecting the + to the + and the - to the - (here it was the Samsung SGH-F480); while the other cellphone was plugged to its charger and while the N900 was plugged to the USB. With that in place I was able to enter the rescue initrd boot mode and later flash the phone as usual.

Effectively it seems to me that the battery was not charging at all because the voltage was to low. Now it is charging normally.

Update:
The problem didn't go away. The orange flashing light seems to not working anymore when the charger or the USB is plugged in. No light appears. After using the phone for a while this morning it just stopped suddenly and the same problem persist.