Reconciliation will be based on the AR account+associated partner so you cannot directly pay an invoice for another partner

Original vouchers are similar to:

DR AR - company B 100

CR sales 100

DR AR - company C 200

CR sales 200

If the mother company is always paying for the children you might want to share the AR account in all partners (but not mandatory see below)

You probably have to go through an intermediate voucher (intercompany payment) such as:

DR AR - Company A 300

CR AR - Company B 100

CR AR - Company C 200

You could simply create a journal with the account AR for company A.

Then you can issue your payment against line 1 and reconcile the other 2 lines with the original invoices

Since partner_id must match to reconcile a payment with an invoice, I have in the past supported this by:

1.  Overriding the definition of res_partner.commercial_partner_id so it can be edited.

2.  Adding commercial_partner_id to a res_partner form view so it shows on the UI.

3.  Telling users that Company B and Company C must be setup with Company A as the Commercial Entity (commercial_partner_id).

Invoices for Company B or Company C will now be booked in the Sales Journal as partner_id = Company A.

When a payment for Company A is entered, invoices for Company A and the two affiliates will show as being able to be paid.