You can have two of the same medications on your pharmacy profile. In your case, this seems to be an issue with the pharmacy identifying a duplicate therapy and cancelling the prescription. Whether or not this was the correct thing to do, I'm not sure based on the information provided.
When a prescription comes into a pharmacy system, it very rarely can be just deleted and in most cases should not be. If it can't be filled for whatever reason (e.g. too early, drug interaction, duplicate therapy), it simply would be "kept on profile" for later filling or simply for reference. In addition, in no situation should a pharmacist simply cancel a prescription without talking to the prescribing doctor. Perhaps there was just a communication error.
It's very common to have two different prescriptions for the same thing on a pharmacy profile. They could be different dosages for different situations for example. Things get a little more complicated when controlled substances are involved, but still, is relatively common. There must be other factors in your situation.
Lastly, it's difficult to ascertain from your question, but perhaps the pharmacy simply cancelled the refills of the prescription on the clonazepam? If this is the case, this may be accurate depending on the state you live in. In New York for example, clonazepam, which is classified a benzodiazepine drug, cannot legally have any refills. It requires a new prescription every time. If you are in a state that does not allow refills, you need to make your doctor aware of this and request a new prescription every time you are due.