What it means is AFTER you trigger part 2, don't craft any MORE desert jewels until after you have collected 50 fragments. Otherwise, the counter resets and you have to start collecting the 50 again.
For part 2, I had 26/50 collected, but I started crafting and my counter went down to 1/50.
Part 2 says "collect" but this is misleading, you actually have to "have" 50 fragments in inventory to complete the task.
(You are correct, the two parts require 75 total. If you collect 50 before completing part one, part two should automatically say you have 25/50, so you should only need to collect 25 more to complete part 2)