Did the Police get back to you with their findings?
Did the police commissioner register an FIR on them?
Basically, a defamation case can be filed only if you have defamed the person in public or society. But filing false complaint against a person will also amount to defamation provided the case is proved otherwise.
See the letter you wrote to the Police Commissioner. If you have mentioned that you "think" your manager might be involved, then you are safe, because your complaint is against the theft and not against any individual, but you are mentioning the managers name to help in investigation. So it doesn't amount to defamation.
As far as harassment goes, you have approached the police regarding the stolen goods and not against any individual. So it's not harassment.
Now suppose Police says that your manager is innocent, then you can still approach the court asking the court to direct the Police to conduct investigation properly.
But what you can immediately do is to file a complaint against the one who has mailed you and is threatening you to file an FIR. No one can threaten saying he will file a police complaint.