For my project, I'm using the VCC pin to output power to an external device. I need VCC to output 3.3V to the external device. Can I open jumper SJ1 to reduce the voltage of the VCC pin without affecting the operation of the other parts of the unit?
I'm pretty sure that, despite the schematic provided, you will find that the 5V Pro Micro actually has a 5V regulator onboard. So even if you open the jumper, it will still be powering the Atmega32u4 at 5V (technically 5V minus diode voltage drop and regulator dropout voltage).
You could change the regulator for a 3.3V one using a hot air station and solder paste and open the jumper, but as other posters have commented, you would still be running the Atmega beyond spec at 16MHz and 3.3V.
I had the same issue on my cheap 5V @ 16Mhz Pro Micro from ebay. I have the 16Mhz crystal and a voltage regulator marked S2PC. The J1 was not bridged and I was only getting 3.3V on the digital pins... wait a sec that should be 5V!! I Went ahead and bridged the J1 jumper and now I am getting 5V on my digital pins! Not sure what is going on behind the scenes with the J1 jumper open with this hardware but I'm thinking it may have been overclocking the chip while running at the lower voltage. Going to let it run over night and see if something doesn't blow but it looks like they may have just forgot to bridge that J1 whilst mass producing both the 3.3V and 5V versions of this board.