The only way I know, if the subtitles have been, 'fused' into a movie, is good only if the subtitles lie at the bottom of the screen. Use TMPGenc and 'clip' (Settings-->Advanvced-->Clip frame) the South screen. The subtitle will be removed, you'll lose the whole clipped part of the screen and the clipped part of the screen be replaced by a black screen (half of it North, half of it South), to re-make the VCD size (in pixels) VCDx x VCDy. If the Video Arange Method is 'Full Screen (keep aspec ratio)' you might want to clip some E/W screen to enlarge the N/S screen (check 'Resized image is used to display preview' an TMPGenc's 'Clip frame' window to see what you're doing).
Ah, what's a skvcd? A SVCD? If so, you'll need the TMPGenc M2V plugin to make it able to load the MPEG-2 file (TMPGenc alone can only load MPEG-1 files; read the 'sticky' tread to lean where you can find it).
