I haven't tried pulling Excel -> SQL with PowerQuery yet, only really dabbled in presenting data the other way. Do you know if this works easily with a document that utilises a lot of macros and VBA? Or are we still talking flat CSV.
What are you talking, Excel with VBA is importing/consuming the data, or it is the datasource for something else?
I assume Excel with VBA is importing/consuming the data in which case Power Query / Power Pivot would likely solve most of your problems. Refactoring a large complicated existing spreadsheet to use PQ rather than your existing peocess, hard to say how tough that would be.