Your locally downloaded BCL content (measures or components) exists in a directory named "BCL" under your user directory on your computer. The typical intent is that it is shared across different versions of OpenStudio you install. If for some reason you have components that you don't want anymore you can start fresh by deleting the BCL directory. A new one will be made the next time you re-launch the OpenStudio application or the Parametric Analysis Tool.
It isn't exactly clear what behavior you are seeing. It sounds like you had 1.6. installed, and you had downloaded some measures from the BCL. Then you un-installed it and re-installed 1.6, and now you don't see the measures that you have before. The Un-installer shouldn't clear out the BCL directory, but that sounds like what you are describing. The only time I could see content disappearing from the applications if you had OpenStudio 1.6, downloaded content that required 1.6 or later, and then installed an older version like OpenStudio 1.5.
If you try re-downlading the measures again does that work, or are you prevented from doing so? If you already had a measure in your database the checkbox to download it would be grayed out.