When playing for free all RTC (Rogue Trader Credits, our virtual currency) bought counts towards the upgrade to the full Premium game.
Free can incrementally be upgraded to Premium with the purchase of a total of 20,000 RTC. You keep those 20,000 RTC to spend, it is not taken for the upgrade. You simply have to past that amount to upgrade to premium.
The progress is limited when playing for free compared to the $20 base version. The $20 version has all classes available and 300℅ boosted progression.
All types of progression, the 2/3rds of your accumulated progression beyond the free version - is banked and unleashed when you upgrade to premium. This means even when you are playing the free version, the progression you would have had as a premium user is waiting for you. We like to be nice about things.