Using old data folder after reinstalling client

I am synchronizing a lot of data (hunderts of gigabytes) to multiple computers using owncloud. I wonder if I can reinstall the operating system and then install again the owncloud client and use the same folder without downloading everything again.

Please note that the station that I am reinstalling contains outdated copy of owncloud data. Some of the files and folders were deleted or moved on the remote and I and I want them to be deleted localy.

The owncloud client allows me to use any folder I select and then it offers me two choises:

  1. Keep local data
  2. Start a clean sync

Is any of these two choices correct? Is somehow ensured that local files which I have locally which were deleted or moved on remote end won’t duplicate?
What about changed files? Won’t it cause conflicts if local copy has outdated file contents?