The answer to your question depends upon the value of the item stolen and your position in the company. If it was a misdemeanor value, they only had two years to initiate prosecution by filing an accusation in court. If it is a felony value, they have four years to file an accusation or indictment. The felony value has recently changed. When you were arrested, the case was a felony if the value of the property taken was more than $500. Now, the felony value has been increased to $1500.
You can also be charged with felony theft if you owed fiduciary duties to the company. This sometimes happens to bookkeepers and accountants, according to the level of trust and control that they have been granted over the money. This is a question of fact based upon all the circumstances. Therefore, in order to give you a more definite answer, you need to hire a lawyer. Ultimately, if you are not prosecuted, you will want a lawyer to help you get the arrest expunged from your record. If you are prosecuted, a lawyer will be able to effectively present your defense.