The Oxford English Dictionary has several meanings, two of which are relevant;
1. Someone who manages something. (Now rare in a general sense).
2. A person who's office it is to manage an organisation, business establishment, or public institution, or part of one, a person with a primarily executive or supervisory function within an organisation, etc; a person controlling the activities of a person or team in sports, entertainment etc.
Each organisation, or indeed individual, is likely have a different view of the meaning. It is not uncommon for people to be called a 'manager' when they don't manage any other people at all.
To my mind it means that someone who has day to day responsibility for a function within an organisation and is not supervised on a daily basis.
However, that's not likely to help you.
I'd have to wonder why the
HR Manager would not help you out by updating the letter, especially given that all you want it for is to undertake further education which can only benefit the business.
The comment your
HR Manager made about you "reassessing your importance within the organisation" sounds like it was meant to belittle you and make you feel insignificant. Frankly if someone said that to me I would start looking for another job!
Will the people who are running the MBA course not accept your current letter? (Have you told them that the person who wrote it is on maternity leave?)