In KeyPay, businesses (or companies) are separate entities. The employees within each business are also separate entities. So, even if John Smith works for both CompanyA and CompanyB, there would be two separate employee entities for him for each company. Submitting timesheets for either employee entity would be under each business, and won’t have anything to do with each other. As such, timesheets in both businesses will not be considered overlapping, even if their times do overlap.
I’m not sure how you’ve set things up so that when you send 2 timesheets, one timesheet overwrites the other, as normally if the timesheets are overlapping, you would get an error code response for the 2nd timesheet, and it won’t be created. But to answer your question, there is no way to modify a submitted timesheet so that it will ignore the overlap check.