Can a school punish students for a legal absence?

On Monday my school had it's "Senior Skip Day" now all students who "skipped" had their parents/guardians call in to make their absence legal. Well my Principal is now saying all students who "skipped" on Monday are having to take zeros for whatever cles they missed which in some cases is causing students to fail a cl that is a graduation requirement. The deal that my principal is setting up is that you have to admit to "skipping" and take a day of in school suspension for the zeros to be erased. Now first the school is making us miss more school and miss lessons plus they are blackmailing us into taking ISS in order to get our grades back despite the fact our parents called in making this perfectly legal. Basically my question is does the school have the right to punish students for a legal absence? This is a public school system in New York state.