Programmatically turn on PIR device with Arduino
PIR sensor amplifies the voltage difference that is created by varying resistance of infrared sensitive detector. If you short it the output voltage appears on input and amplified difference turns it on. It does only for a limited amount of time. It timeout is set for this circuit, it can be activated again after x seconds and the cycle repeats. Please look at the data sheet for PIR detector like this one http://www.onsemi.com/pub_link/Collateral/NCS36000-D.PDF for more information on PIR operation. 

If you really want to turn the PIR on in parallel then you should plug the transistor between PIR input and output, bypassing it, and turn the transistor on with your arduino digital output. This way the opamp will get its VREF at the input, almost as if the sensor got a very strong source of infrared radiation.

Shorting the PIR does not have negative effect over time. But if the circuit has timeout threshold you won't be able to have it 'ON' all the time. For ex. NCS3600 example circuit timeout is 5 sec. and output is on for 1.6s. 
If all you want is controlling the output of PIR you should override it's output instead of controlling the input. 

Hope this helps.