I would keep the original ID numbers from one of the databases and only allocate new ID numbers (or "adjusted ID numbers") to the other (rather than, for example, creating new IDs across the board)
Keeping the original table would mean not adding any new columns for "Original ID number", but you might choose to add a column for "original ID number" during the Import so that you can easily convert, for example, the Emp_ID in the Notes table from "Old" to "New" whilst importing that.
But if you can just add 100,000 to make the "New ID" then I think that is easier [than having to have Old / New conversion columns]