New Backerboard in shower doesnt line up with old cement liner
My best recommendation is to rip out the existing shower floor and the old cement liner and start anew. Then you can rebuild this small "phone booth" sized space to properly work with the new sides and where they join the base. It may be that the use of a cement liner can be completely replaced with a newer technology. After all, if parts of the existing cement liner have basically degraded back to literal sand how sure can you be that that will not continue and have to be replaced in a few more years anyway.