Anything connected to GPIO12? In general, what pins is the GSM module connected to?

You're only flashing the application code. If your ESP32C6 flash is entirely erased, you'll also need to flash the bootloader and partition table.

Also one more instant question, is there any document describing register policy in ISR? For example what registers are automaticaly preserved and how, what registers can be changed and what registers must not be changed and so on. Are there some registers strictly reserved by ESP-IDF. I mean, for ...

That's an issue between the USB-serial chip and your PC, the ESP32 doesn't have anything to do with this and 'factory resetting' won't solve your problem. I don't know enough about Windows drivers to say more; perhaps you need to reinstall the driver or something?

I think that's all part of the lower level MAC/PHY code, and we haven't open-sourced or publicly documented that.

You're likely runnning into issues wrt how the partitions on the chip are defined. In Arduino, you can probably change that under Tools > Partition scheme.

Fwiw, you could also move over to newer chips like the ESP32S3, which have an internal USB-serial-JTAG adapter.

espefuse is a Python script that you can also use as a library in your own Python scripts. Technically I don't think we promise anything about the API we provide there, but I imagine it's going to be more stable (and visible if it breaks) than parsing the output.

The flash generally supports 100000 erases per sector before it wears out and shows errors. How many writes you get out of that depends on what you store and how the wear leveling algorithm behind it does.

That would be the main flash; you can look at the examples/storage/spiffs example to store data there.