Trying to program an STM32 device with ST-LINK_CLI.exe

Here is the simplest possible LED flasher program that works on the STM32VL Discovery board:

/* Test.c
** Simple program for STM32F100RB to flash LED on PC_9
**
*/

#include <stm32f10x.h>

void delay(void);

void main(void)
{
  // I/O port C clock enable
  RCC->APB2ENR = RCC_APB2ENR_IOPCEN;
  // Set PC_9 to output 
  GPIOC->CRH &= ~(GPIO_CRH_MODE9 | GPIO_CRH_CNF9);
  GPIOC->CRH |= GPIO_CRH_MODE9;

  while(1)
  {
    GPIOC->BSRR = (1<<9);
    delay();
    GPIOC->BRR = (1<<9);
    delay();
  }
}

void delay(void)
{
  volatile unsigned int i;

  for (i = 0; i < 20000; i++)
    ;
}

First the programming voltage, it is given in the data sheet under the operating conditions of the memory (page 63):

Vprog Programming voltage 2 - 3.6 V

So if I read your suggestion correct it might have been powered only by that coin cell during programming? This might be very very bad indeed. The controller draws a maximum current during write operation (just the flash) of 7 mA. A small coin cell really doesn't cope well with higher currents and it's voltage as well as the capacity dropped probably really fast. Given the datasheet of a CR1220, the voltage drop on a full battery would be at least 0.5 V if you draw 7 mA from it, so it starts out at about 2.35 V, not much headroom.

But I also wonder if your circuit is fine now - have you measured the current it draws and checked all the voltages and their stability if you draw current (connect a resistor decade and vary it a bit)?

Now a possibility on how you might be able to salvage the part. I guess it won't work as you have no trouble connecting to the device, but anyways:

The F103 has a built in bootloader which is accessible if you pull the BOOT pin high during power up. You will also need access to UART1 to be able to communicate with the bootloader. Have a read of section 3.4 of the reference manual. Another good resource is this document.

If you can connect to it, there is a tool (STSW-MCU005STM32 and STM8 Flash loader demonstrator (UM0462)) available from ST which allows to interface with the bootloader and erase or program the chip.