Nothing can be done
Some people may need the extra, because they don't have all (or any) of the Skill champs that you earn with the final Milestone.
So they would have to run some entries just to reach the Milestone for Skill champs, and the run them again with those champs in order to do those paths where they are needed.
or also (for those that care about getting the Objective Titles), if you ran some additional paths prior to their matching (Hint Objective Title) becoming available, you can go back once those Objective drop each week to get some of those Titles that you otherwise forfeited by running more than 4 times each week (in race to get Milestones, before available Titles).
tbf, you don’t consume them when you do re runs of the science mutant or tech gates. Well mine didn’t I just did it 4 times to unblock the skill 2*
You don't consume them unless you finish the quest. That is confirmed as soon as you use then to enter the quest.
There is also no gate if you go down paths you’ve already completed.
If you do finish but you’ve already done the path, you don’t consume anything.