Additional SQL Server features and topics not covered by specific categories
Amelia suggested that you should also apply CU14 for SQL 2016 SP2. But to be honest, I would not expect that to resolve the issue.
The root problem is that the MDS wizard has an execution timeout which is non-zero. And apparently your table is larger what the timeout permits. Or your hardware is too slow.
I am not very acquainted with MDS, so I'm hesitant to suggest tricks. You could copy the data in this table [mdm].[tbl_3_X_EN] somewhere else and the delete a lot of it before running the wizard. But then you need to know how to put it back. Can be tricky if the schema changes with the upgrade.
You can also look into improving the hardware. If this runs on a VM with humble resources, maybe speak with the IT department if they have something more powerful that you can borrow for a while. Or, if this is at a cloud provider, upsize your environment temporarily.
In my opinion, this is a deficiency in the product, and thus if you open a support case, you should be refunded. This is after all a blocking error.