Looks like you're dealing with unicode characters. This revised code works for me --
#include <Array.au3>
Global $sEML = "Message-ID: <20191203114629.18789103.20749@sailthru.com>"&@CRLF
$sEML &= "Subject: =?utf-8?B?8J+TiCA1IG9mIHRoZSBCZXN0IFN0b2NrcyB0byBCdXkgZm9yIERlY2VtYmVy?="&@CRLF
$sEML &= "MIME-Version: 1.0"&@CRLF
ConsoleWrite(">>> $sEML: "&@CRLF&$sEML&@CRLF)
Global $sSubject = _QuotedPrintable_DecodeEncodedWord($sEML)
ConsoleWrite(">>> $sSubject (_QuotedPrintable_DecodeEncodedWord): "&@CRLF&$sSubject&@CRLF)
$sSubject = StringReplace($sSubject, ChrW(55357) & ChrW(56520), "") ; <---------------------------- ERROR?
ConsoleWrite(">>> $sSubject (StringReplace): "&@CRLF&$sSubject&@CRLF)
Global $aArray = StringSplit($sSubject, "", $STR_NOCOUNT)
For $i = 0 To UBound($aArray)-1
ConsoleWrite($aArray[$i] & " - " & AscW($aArray[$i])& @CR)
Next