Try this. I changed two of the nan to just na to maintain column alignment.

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1186932

use strict;
use warnings;

my $high = 0;

while(<DATA>)
  {
  $high < $_ and $high = $_ for /SATID (\d\d)/g;

  # middle
  s/SATID (\d\d) .{17}SIGNAL \d\d \K {35}(?= SATID (\d\d))/SATID @{[
    $1 + $2 >> 1]} VAL1 na VAL2 nan SIGNAL na/g;

  # beginning
  s/\d:\d\d:\d\d \K {35}(?= SATID (\d\d))/SATID @{[
    $1 - 1]} VAL1 na VAL2 nan SIGNAL na/;

  # end
  while( /.*SATID (\d\d)/ and $1 < $high )
    {
    my $nextnumber = $1 + 1;
    s/$/ SATID $nextnumber VAL1 na VAL2 nan SIGNAL na/;
    }

  print;
  }

__DATA__
Timestamp: 00:47:14 SATID 13 VAL1 28 VAL2 227 SIGNAL 37               
+                      SATID 15 VAL1 22 VAL2 265 SIGNAL 30 SATID 16 VA
+L1 22 VAL2 265 SIGNAL 30
Timestamp: 00:48:14 SATID 13 VAL1 28 VAL2 227 SIGNAL 37               
+                      SATID 15 VAL1 22 VAL2 265 SIGNAL NA SATID 16 VA
+L1 22 VAL2 265 SIGNAL 30
Timestamp: 00:49:14                                     SATID 14 VAL1 
+22 VAL2 265 SIGNAL 30
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