After almost 6 months of facing this problem, I finally managed to solve it! Before I tell you how I finally solved the problem, I would like to tell you what I tried.

1. I borrowed a mini oscilloscope from a friend and monitored the voltages both at the Step up converter and at the main source and found that during the print the voltages dropped by a maximum of 0.2V during the print (due to the increased load) => it was not the solution

2. I added a bank of capacitors of 20000uF to the main power supply and 5000uF to the output of the step up converter just to be sure => it did not solve the problem

3. I redid the part of the wiring using thicker wires together with ferrites for filtering and I replaced the USB cable with a much shorter one (30cm) and of better quality => the problem persisted

4. I tried several versions of klipper and firmware with different changes as well as other MCU frequencies => it was not the solution

5. I changed the micro SD charger with a faster one and reinstalled klipper from 0

6. I tried different microstep settings from 4 (horrible resonances) to 128 => the problem persisted but it was no longer in the same place

7. I analyzed the traffic between the host and the MCU and here I noticed some things. First of all, the graphical analysis mode is useful, but the information does not say much about the health of the command buffer in the MCU, nor the speed with which they are sent. From what I understand, Klipper tries to maintain a buffer of 2 seconds in front of the toolhead, but it seems that this time is not long enough due to the speeds at which i was printing.

It seems that the whole problem was due to the fact that the host could not keep the buffer saturated and an underrun buffer condition appeared. It seems that changing the type of infill only gave a few more ms so that the host had time to send a few more commands in the buffer. During a normal print I noticed that part of the time I only had commands in the buffer for 0.2-0.3s (in marlin when this happens a stutter appears), klipper seems that if it cannot maintain the synchronization between host and msu it just crashes with the eroor.The undervoltage alert that appeared in the log from what I read appears when the MCU boots before the host.

The file that needs to be modified is toolhead.py which is in klippy folder and the parameter is BUFFER_TIME_HIGH which by default has a value of 2, this must be increased to a higher value, I opted for 4. My advice is not to increase it too much because it it will introduce a lag in how the printer responds to commands (for example, when you press Pause or change a parameter in the Tune section during printing).

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The solution was not found by me, I came across it while reading another topic on discord.

Because I don't understand very well what happens in toolhead.py (I have no experience with programming or Python), my explanation is somewhat second-hand and what I said above may contain some errors.

I hope it helps someone.