I'm fairly certain that the points transfer to the currently active path. After I finished the initiation path I had earned ~8 extra tokens, it had automatically chosen the first path but when I changed to another path straight away it showed I had 8 tokens towards the first unlock the now active path. I think you unlock a reward every 10 tokens and it just unlocks on the currently active path, so when you change to another active path you haven't actually progressed 8/10 tokens for that item and instead will just unlock the next item on whatever the currently active path is in 2 more tokens.
Ok, I can confirm this. I switched back to this inactive path after progressing another path, and the points to the next tier changed to match the other path.
