Any experience with disabling the Auto Reset on Serial Connect feature?

I am currently working on a hobby project, using an Arduino Nano to monitor some plants. Basically it is a Window Farming Automation project in its very infancy. It will log the 'vitals' of the window farming plants and possibly in the future be able to feed and water them: HerBot.

I would like to let the HerBot monitor the plants on its own and then connect the computer to it from time to time in order to download the log and occasionally change the batteries, which drives the HerBot.

But ... it resets when I connect the USB back into the Nano. I have been searching the net and found a solution to set the auto reset out of business. One of the references I found was this: http://playground.arduino.cc/Main/DisablingAutoResetOnSerialConnection

Has anybody done this? Any experience is welcome, especially those with a Nano. Does it work? What is/are the trade-off(s)? How do you update the software (can you) on the Arduino, when it is in place?

Thank You all! :-)

Disabling is straight forward. Popping C4 off the board is one way for example. I don't see a solder jumper pad for DTR fro the FTDI chip, that would have been convenient. Once disabled, can press Reset switch during code download when the IDE shows "Compiled xxx ore 32xxx bytes" to restart the bootloader for a download.