It'd help if you gave a link to the program. We don't know it, so with a question this vague, we can't help you yet.
But to me it seems like it should resize them. If it didn't, for example, resize tilesets, one tile would contain four original tiles since RM2K uses 16x16 tiles and RMXP uses 32x32 tiles. It's supposed to resize them, otherwise they wouldn't work properly.