How to prevent nvvidconv from scaling during cropping?

You may try
gst-launch-1.0 filesrc location= Foreman_H264.mp4 ! qtdemux ! h264parse ! omxh264dec ! nvvidconv left=0 right=3840 top=0 bottom=500 ! ‘video/x-raw(memoryNVMM),width=3840,height=500,pixel-aspect-ratio=1/1’ ! omxh264enc ! qtmux ! filesink location=/tmp/cropped.mp4