You need to assign the result of your regex back to lines[i].

for ( int i = 0; i < line.length; i++) {
  line[i] = line[i].replaceAll("[^a-zA-Z]", "").toLowerCase();
}

The issue is that your regex pattern is matching more than just letters, but also matching numbers and the underscore character, as that is what \W does. Replacing this fixes the issue:

String[] stringArray = userString.split("\\P{Alpha}+");

Per the Pattern Javadocs, \W matches any non-word character, where a word character is defined in \w as [a-zA-Z_0-9]. This means that it matches upper and lowercase ASCII letters A - Z & a - z, the numbers 0 - 9, and the underscore character ("_").

The solution would be to use a regex pattern that excludes only the characters you want excluded. Per the pattern documentation could do [^a-zA-Z] or \P{Alpha} to exclude the main 26 upper and lowercase letters. If you want to count letters other than just the 26 ASCII letters (e.g. letters in non-Latin alphabets), you could use \P{IsAlphabetic}.

\p{prop} matches if the input has the property prop, while \P{prop} does not match if the input has that property.

As other answers have pointed out, there are other issues with your code that make it non-idiomatic, but those aren't affecting the correctness of your solution.

Try

return value.replaceAll("[^A-Za-z0-9]", "");

or

return value.replaceAll("[\\W]|_", "");

String[] words = str.replaceAll("[0-9]","").split("\\s"});