How to handle due/to from accounts

It seems that you intend on repaying the inter-co accounts.  If so then I suggest that you create a 'credit card' account in each company to track the transactions.  This sounds odd - but CC entries are a very flexible tool that are well separated from other accounts and are fully reconcilable.

So when the 'other' company makes a payment to your vendor, record it like you paid the vendor using the 'otherCo' CreditCard account.  The otherCo would record a cheque issued to the vendor, but charged to the CC account. Similar but opposite for the refund.  The balance in the CC account is the net inter-advance and should of course be equal amount but opposite value in the two companies accounts.