<a><b><![CDATA[userinput]></b><c>text of c</c><d></d><e>text of e</e></a>

Pattern pattern = Pattern.compile("<b>.*?</b>", Pattern.DOTALL |  Pattern.UNICODE_CASE | Pattern.MULTILINE);
Matcher matcher = pattern.matcher(input);
StringBuilder builder = new StringBuilder();
int lastIndex = 0;
while (matcher.find()) {
    builder.append(input.substring(lastIndex, matcher.start()));
    lastIndex = matcher.end();
}
builder.append(input.substring(lastIndex));

<a><b><![CDATA[test 123 </b><c>inside</c>]></b><c>outside</c><d></d><e>out side</e></a>