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You being a patient and you being an employee are two different things.
Your employer would be a data controller and may access your medical records as a patient, but they should not use them in any way when dealing with you as an employee as you have not authorised them to do so.
You should speak to your employer and raise your concerns so that they are aware of your position, as if they do not comply, they would be in breach of your right to confidentiality as a patient which is against data protection law.
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