Your reconciliation doesn't add up: the total on one side doesn't match the other. Before assuming money is missing, follow this process from the general to the specific — the vast majority of mismatches are explained by filters, dates, or transactions that weren't accounted for, and working in this order saves you from reviewing transaction by transaction from the start.
Steps
Reproduce both sides with the same criteria
Generate both reports again with exactly the same date range and filters. A different filter — only paid payments on one side, all statuses on the other — produces mismatches that look like missing money.
Align time zone and cutoffs
Check that both sides assign transactions to a day using the same criterion. Transactions close to midnight or to the cutoff time are the most common cause of one-day differences.
Compare the amount concepts
Make sure you're comparing gross against gross or net against net. Comparing gross sales against net deposits is off by exactly the period's fees, refunds, and chargebacks.
Look for the items that subtract
Review the period's refund and chargeback reports: their amounts explain differences that don't appear in the payments report. Add those deductions to your comparison.
Isolate the transactions that differ
If the total still doesn't add up, match row by row using the transaction ID or the order reference, and keep only the rows without a match or with different amounts. The total difference should equal the sum of those exceptions.
Expected result
You end up with one of two things: the cause identified (filter, date, amount concept, or a transaction not accounted for) or a concrete list of transactions that differ, with exact IDs and amounts.
Next step
If some transactions remain unexplained, escalate the case with the evidence ready: What information to send to Support about a financial discrepancy.