But how can you eliminate IC transactions related to bank reconciliation? The reconciliation gets the Journal of the bank. what if the bank transaction is an IC payment ? in order to eliminate IC balances in Balance Sheet 

The standard Financial Reports in Odoo can be filtered by Journal. If you always use the same Intercompany Misc Journal then you can check (a) that your eliminations balance and (b) remove them by filtering them out.

Our Consolidation App has a mapping feature (based on GL account) so for complex reports you can specify at the GL account level which transactions to eliminate. This App introduces a consolidation ledger where you can also journal corrections or late adjustments without affecting the GL.