Hi guys...

I have a question... I have :

VW Passat 3BG 1.9TDI AVF 6-speed 96kW 310nm comfortline, year 2001 (model year 2002)
Vw Passat 3BG 1.9TDI AVF 6-speed 96kW 310nm 4Motion highline, year 2004

The older one is tuned to 125kW by a professional guy (and yes, it cost bunch of money). It's more than 1 year old modification, driven more than 30.000 km with it without any problems.

So the question is - would it be possible to read this ECU and flash it into my newer car or are there any differences between manufacturing years and of course, 4 wheel drive ?

I have original VAG (VCDS) for diagnosis and "ebay" galetto 1260 for modification. I have many years of experience with cars and electronics, but I am afraid because I have never done ECU flashing...

Would somebody be so kind and help me with this?

No not good your plan

Always read out first, the make tuning and then write the mod file in your car.

From an year to the next, the car suffers transformations, even the engine code is the same. Same as the PN of the ECU.
Here is an example from audi with your engine.
I have A4 quattro AVF 2002 ecu PN ends with JL and my car has just 1 ventilator-for AC
My cousing a4 quattro avf 2004 ecu PN ends with LJ and car has 2 ventilators for the radiator
same car in 2003 has JT ECU....

So you have to check if you have to check PN of the ecu's. If they are the same, you ca flash the file to your car 4motion and code the ecu as it has fwd. you won't have any error because your 4x4 is mechanical, with torsen.

better to download both maps, compare and look for differrences.