Why are they bad chaecks? Did they bounce? Is the money stolen? If the money belongs to the company, it is unlikely the bank can press charges. If the bank is the vicitm, ie you stole from the bank, it can press charges.
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What do you mean by "bad checks"? If you stole the money, you should pay it back immediately. This way the employer will not report theft and even if they do, the police likely won't act on it.