What are your average nitrate readings?
With regards to the food most Hikari except for Bio-Gold is fairly low end, I would recommend switching to New Life Spectrum Thera exclusively.
Treating HLLE is a long road but it can be done, the pits don't look very deep so as long the problem is corrected the fish will heal.
The other possible issue can be Hexamita which not always present in HLLE cases is Hexamita, These flagellates can interfere in vitamin absorption leading to HLLE. This would need to be treated by Metrozoidale dosed at 250mg per 10g of tank water. Hex also shows other symptoms such as stringy white fecal matter, lethargy, and shrunken body over time. This is a possible cause of HLLE but is not treated the same.
So overall I'd be doing daily 50% water changes, feeding a high quality pellet like NLS, remove any carbon that removed trace elements and you should start seeing improvement in a few weeks.