@Gargron You mean, with a black or transparent box in the middle? You could use ImageMagick's mogrify command to draw it:
https://imagemagick.org/script/command-line-options.php#draw

If you want to remove a horizontal or vertical band in the middle, you could use -copy to move the bottom / rightmost rectangle next to the other one, then crop:
https://imagemagick.org/script/command-line-options.php#copy

@Gargron This maybe helps https://www.imagemagick.org/Usage/crop/#crop_tile_centered

Also, maybe you could create a smaller empty image and paste it centered on the one you want to crop?

@Gargron One way is to make a new image and copy it over to the original in the center.