Mayby I misinterpret something but reading the inline help it sounds like the exact function you are looking for:
After a battery calibration the battery capacity is reduced until the battery is fully charged again. Here you can specify an alternative lower level in this post-calibration phase. Since apc devices remember the time of the last calibration only as a date, the alternative lower level will be applied on the whole day of the calibration until midnight. You can extend this time period with an additional time span to make sure calibrations occuring just before midnight do not trigger false alarms.
I would give it a try