The amount scored in the flowers are counted at the end right?

The scoring elements in the flowers are assessed throughout the match with final assessment taking place at the end of Teleop.
Rule 10.5 Scoring

Also, the points for pollen and nectar in flowers are awarded after all scoring elements and robots have come to rest at the conclusion of the match.
Rule 10.5.2 FLOWER Scoring Criteria

Sources
- BIOBUZZ Game Breakdown: What To Build First, What To Avoid — 10:03 to 12:34 — Brogan M. Pratt
- BIOBUZZ Strategy: How to Win Auto, Teleop, and Flowers — 20:08 to 22:39 — Brogan M. Pratt
- Breaking Down BIOBUZZ Strategies | FTC Live | FIRST Tech Challenge — 20:15 to 22:46 — FUN Robotics Network
- Breaking Down BIOBUZZ Strategies | FTC Live | FIRST Tech Challenge — 22:46 to 25:16 — FUN Robotics Network
- 10.5.2 FLOWER Scoring Criteria