Need help from an experienced QBO Accountant

I work with a Father/Son Home Remodeling business and they work very differently in Quickbooks. And we have three sets of hands in these accounts! The son needs to run his invoicing through the father's Home Services business because of insurance and licensing reasons. When the son gets a new client, he sends them an estimate on the work to be done through Dad's Home Services. As the work is going on, they are sending me receipts and invoices as well as time sheets through expensify. I create a separate invoice with what Dad calls 'a running total' of the exact expenses. When the work is completed, Son then goes into Quickbooks and creates an invoice for the client with the 'projects' that have been completed. For instance: Tile work $1000 (in this total he has figured his costs, labor and profit).  Meanwhile, I've got this running total for that client with the expenses listed out: Labor, Services & Material.  Which is what shows up on the P&L.

What we want do is delete my invoices with the exact expenses. But then, we wondered if it's going to mess up our P&L if we are deleting out the exact expenses for son's all-inclusive expenses. All payments were counted towards invoices sent by son.  I looked in the Chart of Accounts and the son does have the expenses designated as Cost of Goods & Services.

We have maybe 10 clients in Home Services with billing that looks this way.  I'm very confused with this and really need someone to help me figure out how to fix this or even if it doesn't make a difference.

Thanks for your help with this!