After some struggles, I can finally debug the firmware in Eclipse with ATMEL-ICE. Below some hints for other developers who want to debug the RepRapFirmware on Duet3 6HC.
1 - Make sure to flash a debug version of the firmware before you even try to use ICE.
2 - Install 'OpenOCD' and configure it with 'duet3_openocd.cfg' from the RepRapFirmware repository.
3 - Replace the default debugger 'dbg.exe' with 'arm-none-eabi-gdb.exe'
4 - Make sure that the lock bits of the regions 0 to 40 are cleared. If you do a firmware upgrade those bits
will be set. Use Microchip Studio (+ATMEL-ICE) to clear those bits or flash your image with Microchip
Studio.
5 - Set the compiler optimization flag to -Os. (default is -Og).
Now it should work.

Thanks for the super fast response. Next Monday I will give it a try, but also try to understand your solution. I will start simple e.g. two axis and gradually add more axes till the 5 axes + extrusion are running synchronously. I'm especially interested in your generic approach because we will add 2 more axes in future (tilt and rotation of the extruder). Wish you lots of success with your prototype.

After some struggles, I can finally debug the firmware in Eclipse with ATMEL-ICE. Below some hints for other developers who want to debug the RepRapFirmware on Duet3 6HC.
1 - Make sure to flash a debug version of the firmware before you even try to use ICE.
2 - Install 'OpenOCD' and configure it with 'duet3_openocd.cfg' from the RepRapFirmware repository.
3 - Replace the default debugger 'dbg.exe' with 'arm-none-eabi-gdb.exe'
4 - Make sure that the lock bits of the regions 0 to 40 are cleared. If you do a firmware upgrade those bits
will be set. Use Microchip Studio (+ATMEL-ICE) to clear those bits or flash your image with Microchip
Studio.
5 - Set the compiler optimization flag to -Os. (default is -Og).
Now it should work.

@Arplyu In case you want to verify your ICE, the ATMEL utility 'atprogram' has a nice selftest which allows you to test the wiring. You can run it from the command line.

@dc42 That explains a lot. Thanks!

@dc42 Sorry to ask you again about debugging the 6HC. I have a newer board v1.02 where SWD_EXT_RST is removed, so that can't be the problem. The fact that I don't see the 2 MHz SWCLK worries me. Is there anything I can verify (either hardware or software) to get a clue what is wrong? Thanks in advance.

@Arplyu
I have exactly the same problems. Did you find a solution in the mean time?

@dc42 I went through the same process as Arplyu with the same results.
The target voltage is detected but I'm not able to read the device information (from microchip studio)
Looking at the SWCLK line I do not measure a clock, the line is permanently high.
The SWDIO line toggles between 0 and 3.3 volt every second. Reset seems to work.
I also created my own cable. The ATMEL-ICE is brand new so I assume it is ok.
Any hint is welcome, because I'm out of options.

@JoergS5
I would be interested in some more explanation of the algorithms, so yes please, add them to the firmware page.

Thanks for making this intermediate version.
I added some error handling and reporting (just for myself), because it is very easy to make mistakes in configuring the parameters.
I'm working on a simulation environment in CAD to be able to test without having hardware. I found one bug which you may want to repair. If you forget to define a printer (M669 B"<printer type>"), but still define C parameters, the cache will be indexed with a negative index.

Thanks for the super fast response. Next Monday I will give it a try, but also try to understand your solution. I will start simple e.g. two axis and gradually add more axes till the 5 axes + extrusion are running synchronously. I'm especially interested in your generic approach because we will add 2 more axes in future (tilt and rotation of the extruder). Wish you lots of success with your prototype.

@JoergS5
Great ! I'm using a Duet3HC6 + 5x Duet Expansion 1XD, however if you check-in the source code, I can compile myself. Keep you updated on my findings. Thanks.