Have teachers certify/correct attendance for discrepancies before being allowed to submit attendance.
If teachers certify/correct attendance for discrepancies before they submit, this in turn will eliminate having to print out teacher discrepancies and will also make attendance more accurate as they make corrections before they submit attendance.

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Salazar, Demetrio commented
It can work if teachers have to certify attendance before submitting their last period of attendance. They can make corrections or certify before finalizing attendance for that day.
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Guarin, Eric commented
I'd suggest as a popup "you are marking this student present when they have been marked absent" (or the converse) please CONFIRM - THAT could be great! I get so many "discrepancies" due to students coming so late to school and missing entire periods, and due to ditching, that it is really irritating. It would indeed be nice to pre-clear those (and, help catch mistakes as well)
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Avalos, Jennifer commented
THIS ONE IS CRUCIAL!!!!!