Which resistors are taken into account when evaluating the discharge of a capacitor
Why both resistors are taken into account? Isn't the charging voltage
  Vout is charging the upper side only through R1?


If you neglected the reset pin (it's high impedance and with most logic series the current is in the uA range, so it can be neglected) and considered the entire impedance of the resistors and the capacitor on vout it would look like this:

\$ Z_{all} = Z_{r1} + Z_{c1} + Z_{r2}\$

Since this equation uses addition, if you wanted to find the charge time, it wouldn't matter which order these components were it (neglecting ESR of the cap), the charging time would be the same. If the resistors and capacitor were all in series and no reset pin, R1 and R2 could be combined into one resistor. However, you still need to have feedback for the reset pin, so don't do that.