Add 1024 samples of silence to the end of the input:

apad=pad_len=1024

Make sure the audio output will contain at least 10000 samples, pad the input with silence if required:

apad=whole_len=10000

Use ffmpeg to pad the audio input with silence, so that the video stream will always result the shortest and will be converted until the end in the output file when using the 'shortest' option:

ffmpeg -i VIDEO -i AUDIO -filter_complex "[1:0]apad" -shortest OUTPUT