Thank you for reaching out. How far back do these transactions go? If it is more than a year, I would recommend leaving things as they are - the accounting was done based off of the existing data and they need to match the income figures on the filed taxes.
If you know for certain which go to the customer and vendor account, if there are no bills (i.e. open to-be-paid transactions using the existing account), it should be safe to create the separate vendor account and transfer the expenses. Don't touch any of the customer-facing transactions, especially for anything that's on an open invoice.