An employer can change the wages of an at-will employee on a prospective or going forward basis only. The employer must give you notice of the change in wages before it takes effect.
Equally important, an employer may only make deduct from your wages for a purported overpayment, if you have expressly agreed in writing to the deduction. Further, according the Division of Labor Standards Enforcement (DLSE):
[T]here have been several court decisions that significantly restrict an employer’s ability to take an offset against an employee’s wages. Barnhill v. Sanders (1981) 125 Cal.App.3d 1, (Balloon payment on separation of employment to repay employee’s debt to employer is an unlawful deduction even where the employee authorized such payment in writing); CSEA v. State of California (1988) 198 Cal.App.3d 374 (Unlawful to deduct from current payroll for past salary advances that were in error); Hudgins v. Nieman Marcus (1995) 34 Cal.App.4th 1109 (Deductions for unidentified returns from commission sales unlawful.)
If the employer insists you can file a FREE online complaint with the DLSE at:
You have a basis to refuse to repay these alleged overpayments. California law does not allow the employer to deduct disputed amounts of alleged wage overpayments from an employee without their consent. technically, the employer would need to sue you in small claims to recover the alleged overpayments.
The lack of written notice is strong evidence of your rate of pay. Hold your ground if you can without alienating the employer.
Please check the law of your state
The company can change your compensation. However, the more important question is whether the company can require you to repay the $549. Here's what I would do -- File a complaint with the Labor Commissioner. Tell them that the company is attempting to make you repay the alleged debt.