You can attach or link time entries to existing invoices, after-the-fact by using the Progress Billing feature in Core.
If you have already processed and sent invoices to the clients, and then received the approved time entries, you can associate those entries to the previously processed invoices at a later date. You can do so from the Batch Update option in Time Entries by selecting those entries and linking them to that invoice. Core automatically recalculates and adjusts the difference in the value of time entries and invoice amount by generating a write-up/down. Check the Core Help for details on releasing time entries.
You can do the same to expense entries.