File a police report. Your supervisor shouldn't be telling you not to. What they did was illegal and it should be reported to the police.

I had my Adderall stolen while I was in college (a brand-new bottle of 90 pills) and I had to file a police report to have it refilled. It's not only the doctor who might need a copy of the report, but the insurance company. My medical insurance wouldn't let me refill it for my copay without it.

I'm sorry about the ER. They're notorious for not giving out controlled substances prescriptions. It's nothing to do with you, it's just they get so many people in who are drug seeking who say the same thing.