Assuming your SATID sections are all the same length. 

#!/usr/bin/perl

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

use strict;
use warnings;

while(<DATA>)
  {
  s/SATID.{21}(?:(SIGNAL ..)|.{9})/ $1 ? $& : ' ' x length $& /ge;
  print;
  }

__DATA__
Timestamp: 00:55:46     SATID 17 VAL1 49 VAL2 038 SIGNAL 39 SATID 18 S
+ATID 17 VAL1 49 VAL2 038  SATID 19 VAL1 69 VAL2 015 SIGNAL NA        
+                            SATID 39 SATID 28 VAL1 36 VAL2 073 SIGNAL
+ 21

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UPDATE: I think more test cases are needed.

In reply to Re: Preserving "Valid" Data? by tybalt89
in thread Preserving "Valid" Data? by coding1227

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