Hi Liza,
Are these company codes in different countries? If so, the answer is No, they must have different PERNR's. If you have activated Management of Global Employees (MGE) this handled by creating a Person ID to link the two PERNR's via IT0709. If you do not have MGE, you can use the Cross-Country Transfer action to move a person from one country to another, but this creates a termination action and hiring action, but links the two PERNR's.
If the company codes are in the same country, this can be handled several ways. Easiest is to create an additional assignment for the individual or you could create IT0027 to allocate the employee costs to the appropriate company codes in the correct percentages. Either way, only one PERNR for the individual split between two companies.
Paul