Please include the currency code from General Ledger Setup when the Intercompany transaction are posted in LCY (Blank currency code).
Below is how Business Central operates right now:
In this example we have two companies with different LCY. Company A have EUR and Company B have USD.
If Company A have a purchase invoice from a vendor in EUR and want to allocate this cost to Company B and type in intercompany partner and Intercompany account on the document, then when posting and sending the intercompany message; Company B will receive it with empty currency code and therefore this cost will be posted as USD if this is not changed manually in Company B. And this would cause wrong posting.
If the opposite happens and Company B will have a vendor invoice in EUR and want to allocate this to Company A. The documents will be with the currency code EUR. And when Company A received the Intercompany documents it is sent from Company B with currency code EUR but in Company A is stated as blank code as the LCY is EUR.
Therefore if we always include a currency code Business Central will handle each transaction correctly.