I recently did a filter in TES4Edit and found that these mods have critical conflicts so in the interest of a more stable game what should I do here? or am I misunderstanding somt hing

You mean KOTN conflicts with Battlehorn and EQR conflicts with Alt Start?
Both KOTN and Battlehorn (I think?) are official plugins, so the conflicts shouldn't be anything to worry about as long as the load order is correct.
What is the conflict between EQR and Alt Start? If it's only a Quest, then just load Alt Start last.