All of the below comments are prefixed by a big "maybe" - that having been said, here goes; -
Changing the use is defined as development, otherwise you would not need to apply for permission for it - ergo the charge is likely to apply to the area affected.
Extending the premises is defined as development, otherwise you would not need to apply for permission for it - ergo the charge is likely to apply to the area of the new extension.
If you were just changing the use, the levy would only apply to that area of the new use.
If you were just extending, the levy would only apply to that extension area.
As it stands, expect to be hit for both levies on the total area.
That having been said, each local authority is different and you may have get-out clauses [your own comments about it being an existing building refer] or one-or-the-other levy clauses buried in the internal regulations.
In many cases, the charges will only apply to the area proposed to be used - i.e. if you demolished some of the building to facilitate the extension, only the final usable area would be used for the calculation.
One source of useful definitive advice [as opposed to off-the-cuff waffle like this] is your planning officer - ring up and talk it through.
Another source of information are your several elected representatives - they don't bite and you can ring or call into a "clinic".
However, since this is a while ago now, can you post a reply and let us know what happened?