How do I set-up Multiple Canadian Employee Master files in JDE without messing up tax history and ye

I have a public sector E1 9.2 client that need to pay an employee for two different jobs worked that are in 2 different unions with 2 different Employment Insurance (EI) Rates and 2 different pay frequency (BW and Monthly).  I have heard that some have created a dummy SIN number for the second record and then attach the secondary job to that EE master and then at year-end they swap out the SIN Number in the year-end file prior to issuing T4's.  The company has different Corp Tax ID linked to each EI rate.

The client wants to use the same SIN (Tax ID) number in both employee files (ie. duplicate) but I am afraid that it will mess up tax history and T-4 generation so they want to know what the specific issues we would encounter if they did that instead of the Dummy SIN approach.