Hi there: If you started paying the employees in a totally new company then you must carry on and deduct them in the new company until they have reached maximum there. You will be issuing two T4's for them all I assume. One for the previously named/owned company and one for the new company. They will show overdeductions for CPP but they will get any overage back when they file their tax returns next Spring. (Doesn't help them now however.)
The one that loses in this scenario is the new company because any overages for each employee that the employee gets back, the new company will not. So they will seem to be "overpaying" as well.
Is the new name/ownership an actual new entity or simply a purchase of shares of the previous company? You should make sure of what the new structure is just in case Revenue Canada would say that it is the "same" company and employees don't have to start anew with the CPP deductions. But from what you have said it sounds like you do, in which case you have no choice but to keep deducting. Rita Deering