Are you talking about SQL servers implementation of CDC or Epicor’s? We have a specific implementation of CDC that does not use any of the SQL Server features, we self manage it. This was primarily done years ago because of the Microsoft SQL Server SKU requirement to acquire CDC support were beyond the budget of many of our customers.
We have not seen any impact as you mention, but I am interested in learning a bit more so we can research it if it was Epicor’s CDC implementation you were playing with. Prior to 10.2.600 that would require manual manipulation of DB tables and we definitely would not encourage that, but it could have been what you did 