the baseline

BOQ + payment from owner lag  ===>> income part of your cash flow

incurred expenses + payment to suppliers lag ===>> expense part of your cash flow

Lags need not to be equal for every item and expense projections shall be based on expected real costs, it does not necessarily means unbalancing because actual as well as projection might vary from original. What if you estimated borrow material from a quarry but as soon as you start a job a neighbor tells you you can get from his land dirt for free as he needs to dispose of the dirt, a good deal for both.

In any case I would never show my costs to the Owner on the traditional contractual agreement but if Cost Plus then you shall disclose all.

For the baseline you use estimated at time of baseline for the updates you use most recent data. Never disclose your estimated costs on the baseline, just the BOQ (Costs to Owner / Income to Contractor).

If performing job costing within your schedule you might end up adding a cost center to compare budgeted costs against actual projections, very confidential information every bit of it.

In my software [Spider Project] I would model BOQ as a resource while budget, actual and projections as costs so I can purge at a single click of the mouse all costs and submit to owner BOQ modeling only. With formulas would transfer BOQ into a cost account for my cash flow projections, which again are very confidential. Another way to skin this cat can be to keep tow parallel versions of the job one with BOQ only and transfer updates at a single click of the mouse with functionality for this purpose available in my software. Your idea of keeping two sets is not bad, make sure you do not mix them, Murphy is always around.