Is this in the domain config.sh tool? What list do you mean? You need to put in the database instance credentials you self when using the domain configurator.
Do you mean that you use the same database instance, but you can't use the same prefix? If so the database schema's are based on the prefix (dev_soainfra, dev_mds, dev_..., etc.) So you can use a prefix only once for the same database instance.
I don't know if this question/problem is still is opportune? You should probably run the RCU again for the new instance.