Real quick before you run off lore, the debate was whether you continue gaining the catch up cap if you "chip into it" as you put it :P.
Short answer: yes.
Long answer: The catch-up cap is re-calculated from scratch on a weekly basis. It's not that you're earning an extra 1000 points of catch-up cap every week, it's that you're being awarded an amount based on how many weeks the season has been running. It's a minor difference in approach but an important one, as it means there isn't anything to "lose" (or "not gain") to begin with.
To put it another way: every week, you will have 1000 Conquest points for every week (except the first) added to your cap, minus the total number of Conquest points you've earned for the season. If it's week 14 and you've earned 3000 Conquest points already this season, you'll have 10,000 added to your weekly cap. That's done regardless of when you earned those 3000 points.
Hope that helps clarify :)