Hi bdc,
That’s a great question. It is a bit strange for this to happen if you didn’t intentionally switch your employees over to electronic payments. If you haven't approved that setup, it’s a good idea to double-check your linked accounts and your team's payment methods.
Employee payments may be missing from your bank reconciliation if they’ve been sent to the electronic clearing account instead of directly to your main bank account. You can clear the payments from the electronic payment holding queue and post them to your bank account. Take a look at this forum post too, it has some great extra tips.
Cheers,
Princess