Optimizing "complex" iteration over Map with auxiliary maps
Just some points:


I don't see the initialization of choiceCaseAliases,casePaths, or entry. If they are class variables, that's fine, as long as it is meant to be a class variable. If they are outside the method just so that another method can set the values and have the current method run, then it is not okay. If they are class variable just for the method, have them as method arguments.
Here:



    for (String casePath: casePaths) {



and here:


            for (String pathKey: paths.keySet()) {



You don't follow Java conventions. There should be a space before and after the ::

    for (String casePath : casePaths) {


and:

            for (String pathKey : paths.keySet()) {



I wouldn't create a new temporary map for each loop. Instead, I would create one outside the loop, and dump the contents of the temporary map into the map at the end:

private Map&lt;String, String&gt; resolveChoicePaths() {
    String path;
    Map&lt;String, String&gt; tmp = new LinkedHashMap&lt;&gt;();
    for (String casePath : casePaths) {
        String choiceCase = casePath.replaceFirst(".*/([^/]+/)", "$1") + "/";
        boolean mapModified = false;
        for (Iterator entries = choiceCaseAliases.entrySet().iterator(); entries.hasNext();) {
            Map.Entry&lt;String, String&gt; entry = (Map.Entry&lt;String, String&gt;) entries.next();
            if (entry.getKey().contains(choiceCase)) {
                path = entry.getKey().replace(choiceCase, StringUtils.EMPTY);
                tmp.put(path, entry.getValue());
                entries.remove();
                mapModified = true;
            }
        }
        if (!mapModified) {
            for (String pathKey : paths.keySet()) {
                if (pathKey.contains(choiceCase)) {
                    path = pathKey.replace(choiceCase, StringUtils.EMPTY);
                    tmp.put(path, pathKey);
                }
            }
        }
    }
    choiceCaseAliases.putAll(tmp);
    return choiceCaseAliases;
}