I didnt play with both mods as active and didnt notice the conflict. You didnt write more informative about this conflict in description. So, whats the problem with those mods together?
EFF changes the blade rebuilding quest so that it uses the EFF_FreeformSkyHavenTempleAScript instead of the vanilla FreeformSkyHavenTempleAScript. This EFF script overrides the RecruitBlade function and changes it so that the follower being handed to the blades is removed via the EFF framework instead of the vanilla way. After a quick look through the EFF scripts I would guess that if this change is not carried over, any follower recruited to the blades is not properly dismissed.
The conflict with Paarthurnax Quest Expansion is in the record for this quest. EFF changes the scripts, and PQE changes the conditions for the quest dialogue. Depending on load order one of them will win. If EFF wins, I think some of the blades dialogue like dragon hunting won't work if the player chooses the path where Paarthurnax is spared. If PQE wins, the change I described in the first paragraph isn't applied.
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The conflict with Paarthurnax Quest Expansion is in the record for this quest. EFF changes the scripts, and PQE changes the conditions for the quest dialogue. Depending on load order one of them will win. If EFF wins, I think some of the blades dialogue like dragon hunting won't work if the player chooses the path where Paarthurnax is spared. If PQE wins, the change I described in the first paragraph isn't applied.