Intercompany reconciliation checks that what one company says it is owed by another, the other agrees it owes. In Fynease it runs before anything is eliminated, because an elimination on balances that do not agree hides the difference instead of explaining it.
Fynease reads each company's chart of accounts and proposes pairs between two companies of the same client: an account in the Intercompany Receivables group against one in Intercompany Payables, and Intercompany Sales against Intercompany Purchases. Each proposal carries a confidence score. You confirm the pairs that are right and dismiss the rest; nothing is reconciled against an unconfirmed pair.
Sales and purchases between sister companies are often recorded to ordinary accounts receivable and payable, with the sister company set up as a customer or supplier, instead of to intercompany accounts. Scan AR/AP finds them: it matches the customer or supplier on each ledger line against the names of the client's own companies, and lists what it finds. You confirm or dismiss each item. Confirmed items are eliminated on both sides at the group level, the receivable in one company against the payable in the other.
The scan needs the general ledger synced from QuickBooks Online, where each line carries its customer or supplier. A company brought in by trial balance import has no such detail, so its trade balances cannot be scanned.
A correcting entry is booked to the company that is wrong, from the reconciliation itself. It is an ordinary company-level adjusting entry: it is reviewed, and once approved it is written back to that company's QuickBooks Online file. See Write-back to QuickBooks Online.
Charges that repeat, such as a monthly management fee, can be set up once as a template with the lines for both companies, so both sides are booked the same way every month.
It does not eliminate. Elimination happens later, at the group level, when the companies are consolidated. See Elimination entries. For a worked example with a foreign subsidiary and a loan that does not agree, see How to consolidate multiple QuickBooks Online companies.