Most preprint servers allow new versions of the manuscript to be uploaded. Thus, you can update your paper based upon new experiments or input received from the community or through a journal-based peer review process, unless specified otherwise by the journal. For example, on bioRxiv it is quite easy to tell when a new version has been posted, which reduces concerns about multiple versions. However, the original and all subsequent versions of the paper are retained and can be viewed. Most journals will not allow the final copy edited, journal-approved version to be uploaded. Please check the exact policy of the journal to which you submitted your work.