If the program returned 5 lines the first time, and only 2 the next, won't there be lines left over from the first time? How can I tell how many _additional_ lines I got back?

This rather depends on how you have things scoped. If the backticks are in a subroutine that gets called multiple times, each invocation of the routine will get a new array if the backticks line is coded as:   my @lines = `findgsc ...`; If you move the declaration of @lines higher in the script, and then do   @lines = `findgsc ...`; multiple times, each one overwrites @lines with new values. To get a delta on line count (i.e., note additional lines), merely save the prior count. Conceptually,

  @lines = `finedgsc ...`;
  $prevLines = scalar @lines;
  @lines = `findgsc ...`;
  if ( scalar @lines > $prevLines ) {
      # we got more this time
  }
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Note that scalar @lines is the absolute line count, while $#lines is the final index in the array, which will be one less than the absolute count. Which to use is a matter of style, but don't confuse the two.