Q: Is it "The paper was rewritten" or "The paper has been rewritten"?
It seems both could be correct. Please clarify.
Yes, you are right. Both could be correct, depending on the situation and context. Grammatically speaking, the difference between the two is that the first is in past continuous tense and the second is in the present perfect continuous tense. Simply speaking, the first means that some time has passed since the paper was rewritten and the second means that only a bit of time has passed since the paper was rewritten. Perhaps you need to write this in an email to the editor, after making changes based on a revision request from the journal. In that case, it would be better to go with the second, for example, ‘The paper has been rewritten based on your comments.’ Thereafter, you can continue in the same way, such as 'The following changes have been made...'
On a related note, it is better to write mails and other forms of communication and documents in one tense throughout, preferably the simple present or the simple past, as the case may be. However, in manuscripts, different sections need to be written in different tenses. For more understanding of these differences, here are some resources: