Checking in the files will preserve their contents. it is possible that your rebase will need to change the files you have checked out. Checking in your work before rebasing is a best practice and preserves your changes AS ones tied to a non-rebase activity. it may also be required depending on project and stream policies.
Having multiple development views associated with a given stream is often necessary, but keep in mind that rebasing the stream in one view does not update the other views' configurations. So, you will need to remember to manually resync those other views with the stream. Failure to do so can lead to confusion as you will see the rebase changes in one location but not the other.