Q: Does a manuscript rejection imply rejection of the preprint as well?
When I submitted a manuscript, I was advised to register a preprint. If my manuscript is rejected, is the preprint rejected also? And in that case, would my resubmission to another journal be regarded as a duplicate submission?
A pre-print is a completed draft of a scientific manuscript that is uploaded by the author on a public server; often it is the same version of the manuscript that is submitted to a journal. Once the pre-print is uploaded, it goes through a quick check to ascertain that it is scientific in nature. It is then posted online within a day or two without peer review and is made freely available for everyone to view. Since a pre-print is not peer-reviewed, there is no question of rejection unless it is completely unreadable or makes no sense. Therefore, the rejection of your manuscript by the journal will not affect the pre-print in any way. In fact, the pre-print is likely to be posted long before the journal gives its decision on your manuscript.
Revised versions of the same manuscript can be submitted to other journals later. Registering a pre-print is not equivalent to publishing a paper in a peer-reviewed journal; therefore, you can safely submit a manuscript to a journal even if a pre-print has already been registered: this will not be considered duplicate submission. However, it is always good to disclose this at the time of submission and provide the link to the pre-print.