I've heard that before. Often followed later by finding out that something had changed somewhere upstream and there now were duplicates

If you're getting primary key violations then there's already data in the table matching incoming, or there's duplicates in the incoming data. Availability Groups won't cause primary key violations. So in your case, either the truncate is failing, or there's duplicates in the incoming data.

Add some logging to your package to put any data failing into an errors table for analysis and to log any failures of earlier steps. That'll help pin down where the duplicates are.