I was recently asked – Do I need to define an Intercompany Segment in my secondary ledger if the primary it is attached to has an Intercompany Segment?
There is no restriction so you can have same an Intercompany Segment on your primary but not on your secondary. However I would always recommend having an Intercompany segment in both ledgers, the benefits for reporting it gives you apply equally to a secondary ledger as a primary.
If you are using primary as your local ledger and secondary for corporate ledger, the intercompany segment will help you to eliminate intercompany correctly when you consolidate your corporate books.
In short, my advice would be to have an Intercompany segment in the secondary too, you might need the reporting and tracking by this segment in the future and the cost to add it now is much, much less than trying to change your chart of accounts after implementation.