After refreshing a VDB it will revert back to the init parameters which were used during the original provisioning. (Please note that the Delphix Engine will not alert you to this as it is expected behavior as a refresh is seen as a 're-provisioning' from the source database).
Often times a customer will have made modifications in the database's init settings, customizing them (via spfiles etc) for that VDB, and they will have to manually update them again after the refresh
Please note that VDB config templates are only used during provisioning
Option 1 (Recommended):
Using the CLI, dynamically modify the init parameters used during provisions so that a VDB refresh does not revert back to original values (this can be found under source > configparams)
Update the VDB config template to reflect the new values, "drop" and "provision" the VDB using the template to use the new values