In case you are still looking for a solution to make multiple estimates inactive at once, I have a solution in QB Enterprise.  I did the following:

Choose "Customers"

Choose "Income Tracker"

Choose "Unbilled Estimates" tab in the far left upper corner

Mark the estimates to be made inactive

Choose "Batch Actions" Drop Down Menu

Choose "Mark as Inactive"

I discovered that estimates that were dated prior to the closing date I had set in the company file were not eligible for batch options.  

Hope this helps!