Where the Early Bird fee is calculated? Where fees are calculated in Theme code ?

You should look in help_functions.php at function wpestate_booking_price (around line 557).

We use this function to calculate all the fees, discounts etc in 90% of the cases.

The early bird discounts are calculated around line 834

$early_bird_discount = wpestate_early_bird($property_id,$early_bird_percent,$early_bird_days,$from_date_discount,$total_price);

Please note that due to theme update the line numbers might change, but the code will remain the same.

Early bird discount is set in front end submit – edit property

You can set discount in % and the number of days in advance for discount to apply.