As I understand your query, you are an employee and were so before holding the role of company secretary, you are not being asked to resign from the business but have been advised that you will no longer be the company secretary. This is a role you don't appear to want to give up.
In general terms the appointment of the company secretary is the decision of the board of directors. However in your case, it will pay to take some specific advice to ensure that you are being transferred over properly and not suffering a detriment as an employee as your role will alter. That is better done in a conversation as there are a number of questions that need to be asked before advice can be given due to the special nature of the role of company secretary.
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