Need a Java-based solution or, at the worst, command-line for Linux.
I tried to use Ghostscript:
gs -sDEVICE=pdfwrite -dPDFA -dBATCH -dNOPAUSE -dUseC
Here's an example of how you can downsample all (color, gray and mono) images to 72dpi with a Ghostscript commandline:
gs \
-o downsampled.pdf \
-sDEVICE=pdfwrite \
-dDownsampleColorImages=true \
-dDownsampleGrayImages=true \
-dDownsampleMonoImages=true \
-dColorImageResolution=72 \
-dGrayImageResolution=72 \
-dMonoImageResolution=72 \
-dColorImageDownsampleThreshold=1.0 \
-dGrayImageDownsampleThreshold=1.0 \
-dMonoImageDownsampleThreshold=1.0 \
input.pdf
Update:
The *ImageDownsampleThreshold=1.0 parameters enforce that all Images with a resolution higher than the target resolution of 72 dpi will be downsampled. If this parameter is not given (or set to a different value), the default values will be used: *ImageDownsampleThreshold=1.5. This default value will only downsample images with a value of 108 dpi (or higher) and leave the other ones untouched.