Hola Prabhu.
Paratext determines whether references in \r should have parentheses or not based on consistent usage within your project. I mean that there is no configuration space where you can check whether they have parentheses or not. The program analyzes how most references appear: if most are in parentheses, it expects all of them to be; if most do not use them, it expects none of them to have them.
From the message you received, I see that Paratext verifies that most references do not actually have parentheses.
Without further information, I would suggest that you check all the books in your project. For example, if you are currently working only on the New Testament but have the text of the entire Old Testament as a reference, Paratext will take all these books into account when counting whether a reference has parentheses or not.
You can open the marker inventory and search for the marker \r to quickly see which usage is most common.
If you know how to use Regex, you can also count the \r that start with parentheses and those that don't, which will give you the count that Paratext is getting.
If you are absolutely sure of your parenthesis count in \r, I encourage you to file an error report.
Saludos,
Pepe.
