I have a 2007 softail custom,

left hand indicators are not working.

Had new indicator module fitted by HD dealer and wiring checked.

HD dealer is still having trouble finding the problem.

Has anyone had a simular issue or can help with fixing the issue

it should be fairly easy to troubleshoot, there's not too much to go wrong really.
if they're a dealer I bet the first thing they would have done is to change the control unit. [max markup, least effort]

next would be check the globes and sockets individually

then disconnect each end of the wiring loom and check for shorts/opens

There's really nothing else...