This is the difference in I/O wait times after I replaced the faulty Raspberry Pi memory card to brand new one.

So, from about 8-9 seconds AVERAGES to back almost non-existent! Yay!
Steps taken to restore
- Insert the memory card into my Linux laptops memory card reader
- Read the image with ddrescue /dev/mmcblk0 whatsuphome-rpi.img
- Write image to new card with dd if=whatsuphome-rpi.img of=/dev/mmcblk0
- Boot the system, notice that my Python scripts did not work due some problems in Python installation itself, probably some corrupted files in the image
- To fix that, reinstall all the packages with sudo aptitude reinstall '-i'
Done! All seems to be good now. My Home Assistant is up, Zabbix is up, Grafana is up, custom scripts are working. It helped that everything critical is on external USB drive, the memory card pretty much has only the OS.

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