Maybe. For now, the updater is only configured to download silm.pw-specific data files. It will not touch core install data, but it will overwrite existing haks of the same name should you have any. silm.pw always tracks the latest versions of common/shared haks, like CTP. It'll download any missing data files, but it will NOT replace corrupt or handpatched core data files (this may change in the future, but there will be AMPLE warning).
If you are technically inclined, you can see the manifest for the updater here.