Hi KAJH,

No, when you delete the bad debt it will not affect your account. You'll have to make sure that the unpaid transactions accumulated on the correct bad debt account.

Feel free to pin this browser for more information: Write off bad debt in QuickBooks Online.

When you're ready to reconcile the account, you can check this reference: Reconcile account.

You can always post in the forum if you need help about the reconciliation process.