However when installing the vst3 it never asked me for an hr1 file.

You will only be prompted the first time your run the compiled project (either standalone or vst3) as they share the same reference to the samples. I'm guessing when you were prompted to install or locate the samples you selected locate? You needed to select Install which would have extracted the samples from the hr1 file - it's a very clunky system and most of us don't use it.

To solve the issue you need to go to your app data folder and locate the LinkWindows file that points to your samples - delete this file. Then the next time you start the plugin (or standalone) the prompt will reappear and you can select the install option.