Suspension of disbelief requires us to believe that Lincoln has somehow never noticed this protocol put into effect (and that's ignoring the scenarios where it should have been used like with the episode where Lynn becomes Lincolns roommate).
Then problems are made worse because nobody just pulls Lincoln aside for five seconds and just explains things to him. The sisters then escalate the problem further by telling Lincoln to not get involved but then solely make his life miserable forcing him to get involved.
It gets worse when apparently everything is Lincoln's fault and him leaving fixed it, even though he was only responsible for Lori and Leni arguing. Every other argument after was caused by the girls themselves, but again, Lincoln's fault.
The episode where Lynn and Lucy fell out did basically the same concept but executed it far better. And there were generally far better ways to pull off the basic synopsis of the episode itself while addressing the above problems.
To put the icing on the cake, people were expecting a Lori and Leni episode and it to be the best of the four, so there's more expectations shattered than if the Clyde episode (which ended up actually being good) was the bad one of the bunch. It certainly doesn't help it that it's popped up after a string of about four or five great episodes.