Everything you're going to do is going to be a hack and so you're not going to be able to get everything you want. You'll have to pick what you're willing to give up on -- or at least what causes the least disruption.
You can add the negative points as the assignments come in rather than waiting until the end. That way it never goes above 90 in the first place. It also gives them time to question it and for you to remind them that it's capped at 90 points.
Another way to keep them them from "loosing" points that the technically never had is to switch to a weighted gradebook. Make all of the real grades being in an assignment group worth 100% of the grade. Make an assignment group called "Potential Bonus" worth 0% of the grade. Make another assignment group called "Final Bonus" with a single assignment worth 90 points.
The weight on the "Final Bonus" group should be based on your total points. For example, if you have 1000 points possible, then 90/1000 = 0.09 and you should make your final bonus group be worth 9% of the grade. If you had 1500 points, then it would be 90/1500 = 0.06 or 6% of the grade.
Do not put any grades in the Final Bonus category until the semester is over and the other grades have been entered. Doing so will skew the points and make them think they have a higher grade than they do.
At the end of the semester, look at the point totals for the "Potential Bonus" group and put down the smaller of that total or 90 into the single assignment in the "Final Bonus: category.
Doing it this way will not give them any extra credit along the way, it all comes in one lump at the end. But then at least they don't lose the points they never really had.
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