We've made several fixes that might improve the export results in later versions of ArcGIS - though in general our handling of contextual shaping and kashidas in ArcGIS Pro is much better than in ArcMap, as we are not limited by Microsoft GDI.
I'd recommend:
1. Try updating to a more current release of ArcMap (10.6.1 or layer should have the fixes I'm thinking of, current release is 10.7.1)
2. Try importing the MXD into ArcGIS Pro and exporting it from there. You can install ArcGIS Pro alongside any version of ArcMap, and if your Desktop license is current then you also have a license of Pro.
Beyond this, I'd recommend sending this in to Esri tech support so a support tech can more interactively troubleshoot your problem.
Regards,
Jeremy W.