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Employee with complete flexibility of deciding work hour /day, A working hour schedule is defined only to allow system to understand the basic, lunch and OT hours. So according to the requirement the employee gets 30 minutes of lunch if they work 6.5 hours, 

So for example if they work 6.5 hours their actual working hours needs to be 6 hours only, but if they work anything between 6 to 6.49 ( More than 6 hours Less than 6.5 hours  ) hours it will be the actual working time, i.e. if a employees works 6.25 hours the actual will be also 6.25 no lunch needs to be deducted. if they work 6.5 hours it will be 6 working hours and if they work 6.75 hours it will be 6.25 hours of working hours.

This is how Working hour schedule and Flexible day type is setup

Issue - if an employee logs out at or after 6.50 hours of work and before 7 hours (For example if he starts work at 8 am and logs out between 2.30pm to 3pm) the system is not calculating the exact work hours after the deduction of 30 minutes of lunch instead its calculating as 6.5 work hours.  Anytime until 6.5 working hours and at or after 7 hours is not an issue, the system is calculating the work hours after deducting the 0.5 hours for break 

Any ideas on how this can be handled?