How to handle deposits in regards to invoicing?

Hi! I just started as a bookkeeper for an HVAC company that recently opened up, so their processes are not perfect yet. Right now, if it’s a big job that the customer sends a 50% deposit on, they create an invoice that notates the deposit but doesn’t go to the customer. Then when updates are made, job is finished etc., they finalize the invoice & send it to the customer.

The problem is, when those updates are made, their production system updates the invoice date to the current day. So they’ll send me a report for March sales with an invoice for $30k on it, unbeknownst to me that’s just a deposit. Then for example they’ll send me April sales to book, and it has that same invoice# but now it’s $60k. So I have to adjust March sales because AFAIK that $30k should’ve never been there in the first place.

Sounds pretty screwed up because it is. There is 0 intent to double book or cook the books in any way, they are just a little lost and quite frankly so am I. They also got me doing bookkeeping in Excel so it’s all pretty manual.

How should they handle their invoicing to avoid this?