Thanks for getting back into this thread, @AlexisR. I'll clarify things for you so you can proceed with converting your customers to a project in QuickBooks Online (QBO).

Beforehand, please know that I've updated my response above to avoid confusion with the process.

Regarding your concern, all of your transactions related to the sub-customer will also be moved to the projects once converted. Just make sure to select the correct status during the procedure.

Here are some sample screenshots of how the transactions appear on the projects and customer's transaction list: 

Additionally, once you set up your projects, you can track income, expenses, timesheets, and labor costs. You can check out this article to learn more about this option: Track hourly labor costs and profitability by project in QuickBooks Online.

I'd love to get updates on how this goes. You're always welcome to add a comment below if you have further questions about handling projects in QBO. Have a great day!