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Progress percentage is percentage of 'Original Estimate - Time Remaining' (Time Tracking) out of the total 'Original Estimate'. For example, if
Original Estimate = 4h
Remaining Estimate = 8h3h
Progress = (4 - 3)*/4 = 25%
How are Time tracking fields calculated?
In Jira by default, Users can enter any values in Time Spent, Remaining Estimate & Original Estimate. And there is no interdependency between these fields. Except for one place where if both 'Remaining' and 'Original' are set 0, any update to either column will have the same value updated in other column. This add-on maintains the same functionality.