You need to use the PowerPivot functionality of Excel. In the PowerPivot ribbon you can find a Manage Data Model icon. If you open this, a dialog is displayed where you can specify the data type per column. For IDs this needs to be set to "whole number".
In the PowerPivot data model dialog you can also visually manage the releations between different entities.
BTW: if you look at the data in PowerPivot you see that the information is still there, so nothing is lost. Excel just has problems displaying large numbers.
This is the limitation in Excel that long data type is not represented properly (see OData representation). Have you tried to change the column type to string as suggested by Microsoft?
If all else fail, I suggest you to use PowerBI instead.