The CRN is normally done after a conviction or admission into ARD or DDAP. If you are not yet admitted, it is a factor that could be considered in denying entry into the program. More likely, the CRN will be used to determine the level of supervision you require while in the program. Certainly, testing positive for controlled substances or alcohol could be a violation of the program, at which point, depending on the terms of your ARD or DDAP, you may be left with trying the case, pleading guilty, or having a judge resentence you for probation violation. That sentence could obviously involve some jail time.
You should definitely consult with your lawyer on these questions. Your circumstances are unique and more complex than can be addressed here.
Each county district attorney's office sets its own conditions for the ARD program. Urine testing may be a condition of admission into that county's ARD program.
ARD is a rehabilitative program that does not count as a conviction for a DUI offense. If the district attorney's office believes that you failed to comply with the application conditions for the ARD program, then you may not be admitted to the program. Moreover, if you fail to abide by the conditions for the program once you have been admitted, then you will most likely be removed from the program. In either instance, you would still have the right to fight the DUI charge at trial.
The CRN evaluation is mandatory for most counties in Pennsylvania involving an arrest for DUI. If an accussed has no prior record it is often part of the ARD program, but the CRN is often used for all DUI cases, regardless of ARD. At this time, the fact that you test positive should not overly affect your admission to ARD. However, if you continue to fail urine tests you could be removed from the ARD program and potentially face more serious consequences.