The only "flashing" that is done is possibly to enter the VIN. The PCM does not need the VIN to operate. If there is no VIN in the PCM, the ABS lamp will illuminate and the ABS will not function. Everything else will work and the vehicle is driveable. The dealer will charge you 1/2-1 hour labor to flashi in a VIN which will be $50-100.
Note, the VIN in the PCM does not have to match you vehicle's VIN. The PCM just needs to have a VIN in it. Many of us have used PCMs. Also note, the dealer cannot change the VIN in a PCM once it has been entered in it. (I 'm not sure how the rubuilders are doing that) There are a number of people who have purchased PCM from PCM refurbishment places.
Answer one question. Do you have the factory alarm system? When you lock the doors, is there a red secutty light that flashes on the dash?
99 Durango 5.9, FT 4x4, IP stage III w/ K&N air hat, M1, SCT, Fastman TB, 1.7 RR, JBA headers, Borla cat back, Martin Saine valve body, Hotchkis swaybars, Blistein shocks, lowered 2" Black Rhino Kenya wheels, 246. 7 RWHP, 319 TQ