heya, the raid protection plugin would need to exclude the abandoned bases using the EventTerritory API.
if you enable Remove Ownership in the Abandoned Bases plugin then Raid Protection should not protect it as it isn't owned by a player then, skipping the need for it to use the EventTerritory API
no, there is no way to prevent it from converting a base with raid protection. it strictly uses the abandoned time limit set in the config file
furthermore, I'm not sure why you would need both plugins as they effectively do the same thing. except mine works on a strict time limit instead