You should be able to leave the chip in, and tie RESET to GND. This will keep the 328 in RESET state, where it won't listen to (or drive) the serial signals.
lil_satan:
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It seems to me that it is easier to reprogram the Uno again, rather than risk breaking my Atmega328 during removal / re-install.
Opinion: If you want easy, invest in an FTDI module or cable. This is just one of those little things that is as necessary as a DVM for the entry-level workbench.
All that mucking around with jumpers from the UNO to the mini is just fine until the day when you smoke something on the UNO or Mini Pro... then the replacement cost will exceed the FTDI.
Wow! Same - unusual - query twice on the same day, or within a day.
OK, let's see if we can get this sorted.
There are two ICSP headers on the UNO (R3) board, one for the 16U2 USB to TTL converter, and one for the mega328. By placing a jumper between pins 5 and 6 on the latter one, you disable the mega328 in which case all its I/O pins are open and you can connect your Pro Mini TX and Rx to pins 0 and 1 to communicate with the USB to TTL converter. There is no interaction between reset on the mega328 and reset on the 16U2.
So why would there be a suggestion to remove the chip?
Well,
If you remove the chip, you can connect the reset pin (not "GRN") on the Pro Mini to RESET on the UNO and the auto-reset will work perfectly well. Clearly if you have instead grounded RESET on the UNO in order to disable the MCU, you cannot do this and will have to manually reset the Pro Mini using its own reset button, pressing it momentarily when you see the "Done Compiling." message in the aqua (coloured) bar below the code window in the IDE.
Paul__B:
There are two ICSP headers on the UNO (R3) board, one for the 16U2 USB to TTL converter, and one for the mega328. By placing a jumper between pins 5 and 6 on the latter one, you disable the mega328 in which case all its I/O pins are open and you can connect your Pro Mini TX and Rx to pins 0 and 1 to communicate with the USB to TTL converter.
In #11, Reset must be connected to the terminal labelled "GRN" on the Pro Mini.
#12 is correct - with the Reset jumpered on the UNO, you have to use the reset button on the Pro Mini.
Note that the "FTDI" terminals on most "clone" Pro Minis as well as the original "Mini" run in the opposite direction to that shown which is for the original Pro Mini.