Can an employee that is told not to ring up sales by one partner be arrested for accessory to embezzlement?

Sort of a complicated scenario. Possibly yes - possibly no. If the partner was arrested for Embezzlement and it was found that the employee had assisted him in this endeavor - the employee might be arrested also. If the investigation proves that the employee was acting under orders of his boss not to account for certain money then no charges would probably be brought. However - on the other hand - if the investigation leads to the conclusion that the employee was also benefitting from the scheme, then the employee would be charged as an accessory in the crime.