arXiv will keep every version on the website, so people can always go back and see what version 1 or version 2 looked like, even when the paper is on it's 5th version (for example).
These are some places where you can put your pre-prints, and then replace them without a version history being visible to any outsider:
- Academia.edu
- ResearchGate
- Mendeley
- FigShare
- Zenodo
- GitHub (if you delete your version history every time you post a new version)
Also a PDF on your own website can often be picked up by Google Scholar: I've seen this happen to my own papers automatically even when I didn't want it to happen.