When intercompany transactions were already posted to an intercompany account, Eliminate Intercompany Transactions checkbox on the account record will be greyed out and will not be editable. This behavior is by design. This is due to the fact that the amounts posted to the account is already subject for intercompany elimination at the end of the accounting period.
To edit the Eliminate Intercompany Transactions checkbox,
- Navigate to Setup > Accounting > Chart of Accounts
- Edit the intercompany account
- Hit Save
- After hitting Save, click on stop (X) icon on the browser to stop the browser from loading
- Uncheck the Eliminate Intercompany Transactions box
- Hit Save
- Click OK on prompt saying that the you are resubmitting.