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Okay, I got it. Thanks for the clarification GrantSP.

In my mod organizer those merged esps are automatically disabled in the right pane where LOOT sorts the plugins, as shown in the picture below. However, in the left pane those merged esps are still enabled. Are you saying that the bashed patch automatically disables those esps when I launch the game, even if they are still enabled in the left pane? Or should I move those enabled esps in the left pane into the optional esps tab? I am assuming that I should not deactivate the mods entirely because the bashed patch still needs the texture and sound files.

I have been following the Fear and Loathing Step Guide and I have installed all my mods with mod organizer. I followed the instructions given on how to make a bashed patch with Wrye Flash and I created one. As seen below in the picture, 5 of my files were merged and 1 was imported into the bashed patch. I now have my bashed patch in the left pane of mod organizer. Should I disable all the .esps in the left pane of mod organizer that were either merged or imported into the bashed patch? Or should I leave those .esps enabled for it to function properly?

Awesome. Moonlight Tales is functioning properly now. Thanks for the help.

I recently installed mod organizer and went through the step guide. I have also installed SKSE 1.6.16 and SkyUI 4.1. I am trying to the run the mods Werewolf Mastery and Moonlight Tales together. I first installed Moonlight Tales Main 2_05. Then I installed the Werewolf Mastery v3_0 and Moonlight Tales v2_05 Compatibility version. I was never prompted during installation to overwrite any files. I deselected Moonlight Tales Main 2_05 to make sure that its ESP file was not loaded. I used LOOT to sort my mods. However, when I start a new game Moonlight Tales never appears in the MCM menu for SkyUI. When my character acquires lycanthropy he is unable to transform. My character is able to forge and use the Werewolf Customization Ring from Werewolf Mastery. If I add the Moonlight Tales Main ESP to the load order, then when I start a new game I get two Moonlight Tales appearing in the MCM menu. Is there a certain procedure that would allow me to run Moonlight Tales and Werewolf Mastery together in Mod Organizer? I have attached an image of my load order.