Yes! If you remove the app from your device, all data including custom maps and place marks will be lost. We recommend backing up your data regularly, whether it be by exporting your features, backing up your device (iOS only and must be done through iTunes full backup NOT iCloud), in order to prevent any sort of data loss. Maps purchased from the map store can be re-downloaded provided they are linked with a Map Store account (free to acquire and mandatory for Android and Web purchases, iOS it is optional but highly recommended).
If you are having difficulty with the app, we strongly recommend you contact us first before removing so that we can better understand the problem and assist you further.