Given your time format, you don't need to worry about actually handling it as a time. You can just handle it as a string and things will still just work.

while (<LOGFILE>) {
  next unless /\b(\d\d:\d\d:\d\d)\b/;

  if (($1 ge '08:45:00' && $1 le '12:00:00')
   or ($1 ge '14:00:00' && $1 le '17:00:00')) {
    # do stuff.
    # line is in $_, time is in $1
  }
}
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