Pictures? And what is going over the cement board?

I don't see a photo.

So to start with I'll ask was the tub installed in accordance with the manufacturer's installation instructions? Most instructions include how the tub should be secured, and how the tub flange should relate to the tile backer board hung on the walls.

With that out of the way...

My "blind" response?

If the cement board is proud of the tub flange, no worries. The bottom course of wall tile will cover the tub flange. Typically the bottom course of wall tile will be held above the tub deck by the with of a grout line, and that gap will later be filled with a bead of caulk. Often times the caulk can be color- and texture-matched to the grout.

If the tub flange is proud of the cement board, yes, that can be an issue. If it just gets tiled over, the protruding flange can cause the bottom course of wall tile to kick out of plane with the tile above. It'll skew the tiles themselves plus it'll skew the vertical linearity of the tile in the wall-to-wall corners. If there is any movement in the tub, from loading with water, from bathers, any movement in the tub can cause friction squeaks because of differential movement with the tile being in contact with the flange.

If the tub installation is fine, the existing cement board can be removed. 1/4" rips (or whatever thickness is needed) from a 2x4 can be fastened to the edge of each stud to pack out the framing, then the cement board can be reinstalled over the packed out studs so the cement board properly clears the tub flange.

If the tub does not have to be reset, that is my preferred solution.

An alternative would be to thinset and screw a second layer of cement board over the existing cement board. The thinset is there to fill any voids between the two layer to prevent differential movement. The long screws are what will fasten the new cement board to the studs.

Regardless, make sure whatever waterproofing that is to be used on the walls is reconsidered and adjusted if required.

With the photo now being visible, because this is a RedGard shower, I'll remove the option in my previous post of adding a second layer of cement board over the first.

You do not want to cover the RedGard with more board and then RedGard the second layer as well. You never want more than one barrier in a wall assembly.

So I'd review the installation instructions and see what guidance is there and follow it. If that information is not provided, then I'd slice vertically through the RedGard, from ceiling to tub, in the wall corners. I'd remove the wall board that needs to be removed. Pack out the studs, reinstall the backer board, then redo the waterproofing.

The installer should have never let things go this far past the initial error.

See a mistake. Stop. Figure out why the mistake happened. Fix mistake. Move on.