sed -e '/^#/d' <file>
This will not split single lines:
split --line-bytes=<size> <file_to_split>
The size argument is an integer and optional unit (example: 10K is 10*1024). Units are K,M,G,T,P,E,Z,Y (powers of 1024) or KB,MB,… (powers of 1000).
cat <file_to_split>-part-* > <file_to_split>
sort <file> | uniq -u > <new_file>
shred -vn 1 /dev/<device>