Why don’t I see my 6000 plus flowers?

Because volume 5 has been released, your extra flowers have been used to level you up as far as they will take you. You'll find that your level has increased past level 1050, which was the previous maximum. I believe the new max level is 1225. Apparently you still have levels to go, since you need 10 flowers to reach the next level. Regardless, you still can only play 1 chapter per week as the developers create and release it.