Thanks Lukas, I have gone through the notes 1904344 for ENABLE_HANA_MDX and 1902743 for ENABLE_NATIVE_HANA_MODEL respectively, first one is talking about issues with calculations and second one about using Badi, both may not be applicable to me.
My issue, data is cleared in the back end table of BW cube, but still showing up in the EPM report on that model/cube.