My son received a three year sentence on drug charges was released after 13 months did well for a year than got another drug charge . When they send him back to prison will the time he was out on parole still count as part of his sentence or will he have to serve two more years?

Assuming this is in the US, it depends on the sentencing laws of whichever state it is in which he was convicted (or federal laws if it was a federal charge). But my guess is that he may be required to serve the remaining two years (plus whatever the sentence is for the new charge).

If he was on parole, then the time he was out counts on his old sentence. If he was on probation, it does not. He will also have additional time from the new sentence.

Also if he was out on parole, the parole board will have already given him, new release dates, so your son should already know.