ILLMAS has probably hit it on the head. You are probably talking about bank processing time and the payroll is all completed at the same time. The paper checks are issued on Friday and the submission to the bank is on Friday, maybe after COB. A couple of business days to process, Monday and Tuesday, and the funds are available on Wednesday. If the pay period ends on Thursday, there is no solution to this problem. I mean, it can stay the same, they can get paper checks on Friday or the employer can make them all do direct deposit and they will all get it on Wednesday.
Out of curiosity, is this your issue in trying to protect your client or are the employees complaining? If all is legal, I would simply counsel the employer to make the direct deposit the company method and offer the paper check as the option. In that way, the employees can't complain (after all they take the paper check option), it is within the legal time frame to pay the employees and the employer does not have to mess with changing cutoff times. In essence, the employer does not have to change anything.