Hello, @marieke1.
To successfully mark a customer as inactive, you must first delete any projects associated with that customer. To delete a project, remove all time entries linked to it. Also, if there are any unbilled charges, you won't be able to make the customer inactive.
Before deleting the project, we can print or export the Project Profitability report to save its data. However, even if you delete the project, you can still run the Project Profitability report to view the data marked as Deleted.
For invoices/transactions linked to the inactive one, they will remain on your books. The transactions can still be shown in reports filtered by the customer. Reports such as Sales by Customer Detail or Transaction list by Customer.
If you have lots of customers to delete, you can follow the steps provided in this article: Delete customers in QuickBooks.
We know this can be a tough process. We're just a message away if you need more guidance.