How do I control a conveyor to start and stop in same location using optical rotary encoder
Although your solution would work, it seems open to problems such as missed clicks, starting at a different place etc.
A better, more robust and error free solution might be to use a hall sensor.
Essentially what a hall sensor does is close a switch when a megnetic force is applied. So all you have to do is add a magnet to your conveyor/chain. This way, you can easily control where you want it to stop just by moving the magnet, and it doesn't matter what the starting position is because it will always stop as soon as the megnet reaches the sensor.