By definition, a salaried employee is entitled to the same rate of pay regardless of the quality or quantity of work performed. However, if an employee misses a WHOLE day for personal or health reasons, employers may deduct a pro rata share of that employee's salary to account for the missed day. (E.g., if an employee misses one full day in a pay period that has ten work days, their employer can deducted 10% of their salary)
Since you were working during your medical leave, albeit in a limited capacity, you were entitled to your ordinary compensation for such days. Your employer could conceivably "cash out" your vacation during this time (they can do that at any time since they control how and when accrued vacation can be used), but they must pay you for those accrued vacation days in ADDITION
to your regular salary.
By paying your vacation in place of salary to which you were entitled, your employer (depending on how you look at it) is either forcing you to forfeit accrued vacation, which is illegal in California, or they are refusing to pay wages earned.
In either case, you have a claim for unpaid compensation which can be pursued through either California's Department of Labor Standards Enforcement or in civil court. As a prevailing plaintiff in civil court you would be entitled to attorney fees and costs. The DLSE "wage claim" process is free.
To locate a local employment law attorney who can assist you, see here: http://www.cela.org/?page=4
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