Here's code used by one of our tools.  You will need to modify this code.  The main things it does are:

1) Uses setDynamic to set the new value.

2) Throw away Declare_CachedDataSystemSettings page so new value is picked up right away instead of later.

/Eric

String owningRuleSet = "Pega-ProCom";
PublicAPI tools=ThreadContainer.get().getPublicAPI();
if (tools == null) throw new PRAppRuntimeException("Pega-RULES", 0,
    "Unable to get tools");

boolean retValue = ((PegaAPI)tools).getSystemSettings().setDynamic(owningRuleSet,
    trackSavesName, "false");
// clear cache so our new value is seen immediately
ClipboardPage cachedSettings = tools.findPage("Declare_CachedDataSystemSettings");
if (null != cachedSettings) cachedSettings.removeFromClipboard ();

Please check if the OOTB activity @baseclass.pxSetDynamicSystemSetting is of any help to you. Maybe you can copy the java code used in step 1 of this activity into a function.

String owningRuleSet = tools.getParamValue("owningRuleSet");

String setting = tools.getParamValue("setting");

String value = tools.getParamValue("value");

result = tools.getSystemSettings().setDynamic(owningRuleSet, setting, value);