I've now implemented the code to boot with a sequence on the serial port and also an emergency boot when a pin port is held to ground. It's better but sometimes, when programming, FlashMagic return an error message.
This sounds as if a) you have a serial comm problem ( I rememeber one that it took a while to catch - a 100nf cap 232 chip was specified and a 1uF cap 232 chip was installed) or b) the Redmondians strike again, you write "FlashMagic with Windows XP ... Andrew Ayre has corrected". Please allow me to correct your language "has corrected" should be changed to "has adapted to the latest screwup from Redmond"

As this useful ISP function is regulary not working due to the bootvector lost(always after a failure in programming)
Well you state that you have conquered it.

What will be the solution if I'm using some soldered chips in field application and that I can't recover the ISP feature ? hat's why I have to investigate a little more
While I applaud your thoroughness in testing before comitting, let me assure you that with the methods I have described, I have not lost a chip.

Note that since I've implemented the IAP code, I've not crashed any chip, but I4ve to continue and check.
Congrats

Erik