There are two 'classes' of cement board, and HardieBacker is in the class called fiber cement boards. That type CANNOT be embedded in the shower pan, which poses its own problems in fastening the bottom since there can not be any fasteners within 2" above the top of the curb, so that leaves the bottom section flapping in the breeze!
Second big thing...is the liner flat on the floor, or was a preslope installed first? The later is the only way approved by plumbing codes (the liner is the waterproofing layer in the pan, and code calls for that to be sloped to the drain which it can't be if flat on the floor!).
But, assuming everything else was done right: dam corners on the curb, NO fasteners through the liner anywhere inside, on the top, and ONLY low on the outside except no lower than 2" above the curb, AND they did a flood test to verify that the liner was intact...it should work.
Hassle is that one study indicated that 70-80% of the tiled showers built in the USA are not done to industry standards...that's pretty sad, but true!
The HardieBacker should terminate at least 1/4" above the top of the setting bed - that's not the liner, that's the mudbed on top of the liner. If the HardieBacker has a vapor barrier behind it (plastic sheet or roofing felt), you don't need to do anything to the bottom edge.
James Hardie has instructions on their website, and you can get the industry guidelines at
www.tcna.org. The latter is the industry bible, but product specs give sometimes more specific instructions.
I suggest you check out
www.johnbridge.com for help in building a shower that will last without issues.