So, seems the game will load core files in the mod directory regardless of where they stand.
I took coreabilities
created 2 additional copies
coreabilities_blood - I removed everything but the racial blood traits
coreabilities_no_blood - I removed all racial blood traites
I backed up the base core abilities
I took the blood version, renamed it back to base and put it in the game folder (not the mod folder)
I took the no_blood version, renamed it back to base and put it in the mods folder
Seems to work fine now.
Initially I had 3x the abilities since I had the base, blood, and original all in a random folder in the mods directory.
I moved out the base and blood versions to be outside the mods directory and it seems to only be applying 1x the ability now.
So now I have my updated abilities, my new abilities, my original abilites and my racials - all working... it seems