Não é fácil com sed
, mas
awk 'NR%2 {fname = sprintf("file%d.txt", ++n)} {print > fname}' main.txt
dando
head file*.txt
==> file1.txt <==
/F/FID/FID/000001/0/20180215//1/2/
/F/FID/FID/000002/0/20180215//1/2/
==> file2.txt <==
/F/FID/FID/000003/0/20180215//1/2/
/F/FID/FID/000004/0/20180215//1/2/
==> file3.txt <==
/F/FID/FID/000005/0/20180215//1/2/
/F/FID/FID/000006/0/20180215//1/2/
Alternativamente,
split --lines=2 --numeric-suffixes=1 --suffix-length=1 --additional-suffix='.txt' main.txt 'file'
(algumas dessas opções podem ser específicas para a versão GNU de split
).