I've got you some insights about deleted SKU of your products in QuickBooks Commerce in Online, @sue-focusonfashi.
With Commerce tools, you can control your orders, inventory, and sales data for your online channels. When it’s time for accounting, QuickBooks Online will help you track your income and expenses. This will give you a view of your overall business performance and help you stay ready for tax time.
It's possible that when you deleted the SKU in your QuickBooks Commerce, it didn't reflect on your QuickBooks Online.
To fix this, we can delete it manually in your QuickBooks Online.
Here's how:
- Go to the Settings ⚙ menu and then select Products and Services.
- Find the item, then choose Edit from the Action column.
- In the SKU section, remove the info.
- Once done, click Save and close.

In addition to that, let me share these articles to help you manage your product and services in QuickBooks. It provides some idea on how to set up your inventory to reflect your business type.
If there's anything else I can help you handle your product and service items in QuickBooks, please tag me directly. I'll be sure to get back to you. Have a good day!