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I have a Polo 6R1 with 1.6 TDI 90hp CAYB engine. I am experiencing some weird behavior but there is no error code stored in the ECU.

Firstly, there is intermittent rough idle issue. Sometimes car runs very smooth without any shaking. Sometimes it runs smooth, starts shaking for a short time, returns back to normal and repeats the cycle.

The bigger issue is during the regeneration. When in regen, when I give a constant throttle at stand still to keep the RPM between 1-2k, engine speed sweeps periodically by 200-300 rpm. Car is shaking while crusing in regen at engine RPM between 1-2k. Above 2k RPM, there is no problem, car is running smooth. It also stalled twice when I pushed clutch while crusing in regeneration. Engine shut off immediately when I pushed the clutch without any shaking.

Here is the video of the RPM sweep:
https://youtu.be/-Z2EnaejpEg

And here is the ECU data I recorded:
https://youtu.be/godL8XhzuEU

Some plots were overlapping because of the limited space. Below is the explanation of the plots in the video. When giving constant throttle, injection error is 0. EGR is closed and throttle body is around 20%. O2 sensor output, MAF flow and throttle body follows the RPM sweep.
Here is the data for idle in regen. At idle, RPM is at 1k, no sweeping no shaking. EGR is closed and injection errors increase.
Here is the data for idle in normal operation as well. There is no shaking in this data. EGR is active. Throttle body goes back to normal opening. Injection error is very close to 0. I took the car to a workshop and visual inspection showed that EGR was changed recently. I own the car for a year now and I am not sure about the history of the repairs.

Any similar experience or ideas what could cause this behavior?

Thank you very much in advance for your help.

Bad injectors, look at the deviations in regen. 5 mg deviation is a lot.

True, injection deviation is a lot at idle during regen. But it is almost 0 when given some throttle in the regen and it is always close to 0 outside regen operation. Do you think it is stemming from the injectors? I couldn't explain why the deviation is high only at regeneration idling.

yes but idle compensation will only occur at idle. even if you feather the throttle, it will become zero. what are your values when you are at idle without regen?

I thought ECU was continuously monitoring the injection rate and adjusting accordingly. Reading with throttle is not valid in that case.

Injection error readings without regen are around 0.1-0.3mg/str. I attached 2 examples.

Since RPM sweep with constant throttle happens only in regen, I was thinking it was related to EGR. That is why, I thought regen correction values would be large if EGR is leaking at 0% duty cycle and ECU would try to compensate for this additional air from the readings at the O2 sensor. I know more about petrol engines but not that much about diesels. Can an air leakage or EGR leakage cause issues in diesels? I don't think there is a required air-to-fuel ratio range for diesels, so I am not sure how diesel engines monitor and compensate for injection errors.

While car is idling smooth without regen, it seems EGR duty cycle is very smooth, no jumps. And when idle is rough, it seems EGR is jumping 1-2%. Could such a small jump cause rough idle?

I also caught the moment when regen mode ended and car returned to normal. Here is the data of this moment:

yes EGR can cause a lot of issues in partial load and regen but they will also occur at idle and will certainly show up in a scan
air leaks in a diesel are not a major cause of concern since the air/fuel ratio doesn't really matter. you can have 20:1, 50:1 or 100:1, it runs fine...
in a petrol you need the AFR to closely match 1:18 or something otherwise you'll get lean or rich burning. diesels always have excess air anyway.

but if your EGR is leaking, you'll have a P0405 or other P040x code sooner or later, and you don't have it, so I think EGR is fine.

Are normal operation injection corrections good? 0.2-0.3 seems fine to me but I am not sure what the normal range is.

At idle in regen, some diesel designs inject fuel in exhaust or delay the injection time to push some unburnt fuel to exhaust and heat it up. Is this the case for TDI engines? Can this be the reason of high injection correction occurring only in regen?

Is there any resource you could suggest for me to learn more about regen operation in TDI engines, like a self study document? I think RPM sweep at constant throttle and high injection correction happening only in regen is telling a story but I need to know the differences between normal and regen operation to find the suspect, or at least go in the right direction.

from personal experience its okay. I had -0.70 and I had no issues like you.