aldozan:
From Fig 1 I cannot understand where I should connect R2 to. I assume that what in Fig 1 is called 1-wire Network is the connection to the PIN I defined in the Arduino instruction OneWire (e.g. OneWire ow(49)). Ground is ground. But where is the wire to R2 coming from? In Fig 1 it comes from a generic Microcontroller box, but where should I connect this wire to Arduino? Ground, Vcc or where?
It's really not explained properly in that app note. The convention with that sort of diagram is that anything coming out the side of a "microcontroller" box is an active I/O pin. So it looks like they are suggesting that you drive the outgoing communications from the master through the second pin, through the 3.3k resistor. That would slow down the outgoing data transitions so that you don't get harsh ringing.
Sending 1-wire on one pin and receiving it on another pin would take some serious modification of the Arduino library. I don't think it's practical to do this.
On a Teensy 3.x you can actually modify the "drive strength" so that you reduce the slew rate. I think it's also possible on an Arduino Due but it's a while since I looked at that part of the datasheet. Probably not an option for you.
The "appendix B" option is going to work a whole lot better with a standard Arduino and the standard library. You either need an oscilloscope to check on the waveform produced or you need to experiment with different capacitors.
A 1-wire network is loaded down by the parasite-powered devices. If you can reduce the number of them by powering at least some of them from a separate power wire, you will improve the network reliability significantly. I would try that first.