Входной файл

797     47      M797    1       365.0   0.05    0.05    A       0.825
798     47      M798    1       365.0   0.05    0.05    A       0.825
799     47      M799    1       365.0   0.70    0.70    A       0.404
800     47      M800    1       365.0   0.00    0.00    A       0.990
801     47      M802    1       365.0   0.29    0.29    A       0.591
802     47      M804    1       365.0   0.12    0.12    A       0.726
803     47      M807    1       365.0   0.12    0.12    A       0.726
804     47      M808    1       365.0   0.12    0.12    A       0.726
805     47      M812    1       365.0   0.12    0.12    A       0.726
806     47      M813    1       365.0   0.12    0.12    A       0.726

Код

#!/usr/bin/awk -f
BEGIN{ al=790               # added lines at start
       ap=0                 # appended lines (missing)
     }
{
    lc=$1                # line counter
    $1=lc+ap             # adjust line number
    mr=substr($3,2,6)    # marker
    while( NR+al+ap < lc ){ print "added ++" ++al, ap,"lc=" lc}
    while( NR+al+ap < mr ){ print $1; $1=lc+(++ap); }
    if   ( lc+ap   == mr ){ print }
    if   ( lc+ap    > mr ){ print "errorerror"; exit}
}

Выход

added ++791 0 lc=797
added ++792 0 lc=797
added ++793 0 lc=797
added ++794 0 lc=797
added ++795 0 lc=797
added ++796 0 lc=797
797 47 M797 1 365.0 0.05 0.05 A 0.825
798 47 M798 1 365.0 0.05 0.05 A 0.825
799 47 M799 1 365.0 0.70 0.70 A 0.404
800 47 M800 1 365.0 0.00 0.00 A 0.990
801
802 47 M802 1 365.0 0.29 0.29 A 0.591
803
804 47 M804 1 365.0 0.12 0.12 A 0.726
805
806
807 47 M807 1 365.0 0.12 0.12 A 0.726
808 47 M808 1 365.0 0.12 0.12 A 0.726
809
810
811
812 47 M812 1 365.0 0.12 0.12 A 0.726
813 47 M813 1 365.0 0.12 0.12 A 0.726