the outputs resets the chip it turns to an input and all bets are off.
Thanks everyone, this has been a great help to me. After much research I have come to the conclusion that using rs485 is the answer. I was resistant at first, but after researching it actually doesn't seem like it will be too difficult. The needed hardware is also much cheaper than I thought it would be. I have ordered a batch of tlc5940s for about $1.10 each, atmega328p batch for $1.20 each, and the max485 for $0.18 each. With a few of the small extra parts needed, I might be able to have addressable long range 16 channel pwm led nodes for under $4 each. That would be amazing...if it works
I don't actually need to reprogram the chips remotely, I just want it to be easy to do the initial programming.
It sounds like I will be able to upload the sketch through the max485 as long as I manually reset the atmega first. Is that correct?