I'm confused, you're saying it can only be done individually but one of the comments here gives instructions on batch inactivating and it works. Please clarify.

That user's instruction is copied below:

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"