Yes. It doesn't matter what SEP-IRA owned by an individual employee receives the SEP contributions. SEP-IRAs are owned by the individual, so all of the SEP-IRAs owned by the individual can be thought of in aggregate as if they were a single SEP-IRA. However, splitting the SEP contributions required to be made for a particular employee could create an accounting headache, particularly if the SEP plan is managed by a third party such as a payroll processing firm.
You can't have two different SEP plans at the same time, though. Eligibility requirements and the contribution rate as a function of compensation for all eligible employees must be the same.