Consider placing a sign in the rear window that states "Tag stolen" and list your current tag number, also state that a replacement has been ordered. That should put them on notice that your car is not abandoned and that the car is registered.
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Your registration that your keep in your glove box indicates that you have valid registration. In addition, keep a copy of the police report with you in the vehicle showing that the tag was reported stolen. This will not prohibit you from being stopped by the police but will assist you in avoiding being cited for the offense.
Mr. Chen and Mr. Daniels offer you the best advice for trying to handle this on your own. You may want to consider constantly writing letters to create a paper trail of your efforts to inform them of what happened to your tags. If they do improperly order your car towed, you may need to ask an attorney to look into what your legal remedies are in that situation.
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