I can't tell exactly what you mean by features and installing the same setup twice, but:
You cannot install the same MSI setup twice. It's already installed (the ProductCode) so it will go into maintenance/repair mode. This may do a repair/reinstall or, if you've authored it for feature maintenance, then Windows will again notice that the product is already installed but offer the standard feature dialog which lets you add features from the setup, and this latter mode is exactly what you get if you go to Programs&Features and choose change. In other words a true feature maintenance setup offers the feature selection dialog primarily from Programs&Features, and in your scenario with adding two features you'd simply use Change from Programs&Features and not attempt to reinstall the same setup.
Your post refers to Components and RemoveFile, and you should definitely not need to do any of this. If you're not using true Windows Installer features and have built a Component-based setup where Component installation is based on conditions then that would explain what you are seeing. The property values used for your conditions are not preserved so when you attempt to install the same setup again it goes into maintenance reinstall mode for the currently installed product, the property values are empty, the conditions are false, so those components are removed.
Having said all that, you haven't posted your WiX, and the fact that you're attempting to install the same setup twice implies you may not be familiar with maintenance, features and components. In summary, it seems that you should be using the WixUI_FeatureTree dialog set, grouping your components into features to achieve what you're looking for.
If your aim is to replace files that need updating then you should look at the WiX MajorUpgrade element. If you set MigrateFeatures to yes then the upgrade will result in the same features still be installed after the upgrade. Schedule afterInstallExecute is probably what you want. Increment file versions of files you want updating, use a new ProductCode, increment the ProductVersion in the first three fields and use the same UpgradeCode. Alternatively you could look at creating a patch, an msp file.