A fraud investigation can lead to the loss of employees by tipping off the person who committed the fraud. This person could change the records to make someone else look guilty. The employee who committed the fraud should get fired, also other good employees might feel threatened or stressed over the whole investigation and leave.

In pursuing a fraud investigation, the company can be questioned by customers. Is this company good to do business with? The loss of customers might not be worth the pursing of charges and everything going out in public with a trial.

If the victim would tip off the other employees that an investigation is going on it can ruin an investigation.

I think it all depends on how big of loss the company has had due to the fraud if it is worth pursuing an investigation, or just fire who is doing it.