as in changing the old palette to a new palette?
what is the file type of the old palette?
what style is the image gba4bpp or gba8bpp?
as the amount of data held by the palette will change according to which one the image is viewed under.
you could use infranview to create a windows.pal which you would then import in ct2 or in ct2 directly import the palette from the image you are about to import. (I have had mixed success with both).
it largely depends on the type of image.
one you have imported the pallete you have to go to a specific spot in the hex viewer and then go to edit - palette to data. but before you do that you should answer the questions. as you also have to be in a specifc spot in the palette pane on the palette to import export it right.
if you import a gba8bpp palette over a gba4bpp palette you are going to have trouble as the 4bpp palette is smaller. thus you will be overwriting stuff after its smaller pallete that belongs to another file.
if you import a gba4bpp palette over a gba8bpp palette the image is going to be displayed in game wrong (very wrong), as all the colours needed for it to display are not there.
there is more we can talk about here... but i'll wait until the questions are answered.