I've discovered that it's possible to force update.txt execution while flashing boot.bin from RGN.
The good news is that the firmware isn't involved at all, so we can use it for curing.
You can do this it the following way:
1) Patch the boot.bin
1.1) Find bytes 0C 80 A0 E1 at the beginning of the boot.bin. Note, these bytes have to be four-byte aligned.
1.2) Replace the bytes with 0C 80 A0 E3
2) Prepare & copy update.txt into its usual place on SD card, then insert that SD card into your device
3) make RGN from the boot.bin and flash it
4) update.txt is executed