Client imports his invoices from Quoteworks to QBO , I’ve been able to export an invoice even if one there already exists with the same Invoice number, no warning in QBO

We got you here in the Community, @catherine-boweac. Let me provide you with the information you need to get your concerns sorted out.
 

You'll see a prompt for duplicate transaction numbers if the Custom Transaction Numbers feature is on. Take a look at the screenshot below for reference.


 

Follow the steps below to turn on and off the Custom transaction numbers feature:
 

1. Click the Gear icon and select Account and settings.
2. Choose Sales and tap the Edit ✎ icon in the Sales form content section.
3. Select Custom transaction numbers radio button to turn it on/off.
4. Click Save and then, Done.
   
   

If you want to void or delete transactions in QuickBooks Online you can check this article.
 

Please let me know if you have any more clarifications about invoices. It will be my pleasure to help you out. Take care, and have good one!