It is inefficient to read the input file twice. It doesn't matter if the file is small, but it is easy enough to do everything in a single pass over the file.

If the data you want to remove is a fixed width at the end of the line, you can use substr - you don't need substitution.

use strict;  
use warnings;  

my $line = <DATA>;

while(<DATA>) {
    if(/^sb1 1.0 142r$/) {
        print substr($line, 0, -13) . "\n";
    } else {
        print $line;
    }
    $line = $_;
}
print $line;

__DATA__
lines before the changed section
4.62399E+09 2.90871E+09 7.17338E+14
sb1 1.0 142r
lines after the changed section
another instance of the lines to be changed
4.62399E+09 2.90871E+09 7.17338E+14
sb1 1.0 142r
another line with 7.17338E+14 in it
the rest of the file
[download]

produces

lines before the changed section
4.62399E+09 2.90871E+09
sb1 1.0 142r
lines after the changed section
another instance of the lines to be changed
4.62399E+09 2.90871E+09
sb1 1.0 142r
another line with 7.17338E+14 in it
the rest of the file
[download]

Notice that the output still contains 7.17338E+14. Simple grepping the output file for this value is not a good test for whether the file was changed unless you know the value can't appear elsewhere in the file. I would use diff to see if two text files were different.

Notice also that the file may be changed in more than one place. This may not be what you want.

update: if(/^sb1 1.0 142r$/) { is incorrect. There are many alternatives, including if(/^sb1 1\.0 142r$/) { and if($_ eq 'sb1 1.0 142r') {.