I'm using the mod Skyrim Redone which makes extensive modifications to the perk trees. I wanted to make some additions to the Smithing tree, but wanted to do so in my own plugin so I don't have to redo it every time I update Skyrim Redone. I added one perk to the tree and when I tested it, it caused four other perks to disappear from the tree, three of which were completely unconnected to the one I added. If I make the addition in the Skyrim Redone esp that modifies the perk trees, it works fine.

Can anyone give me advice on why modifying the perk tree in a separate esp would break it, and if there's anything I can do to fix it?

If "Skyrim Redone" is not a .esm file, you'll have to update *it* instead of using your own.

If it is a .esm file, then use that as your master file in the CK to make your plugin.

Ah, okay, thanks. It's an esp, so there's no way around it, then?

You can ESMify the Skyrim Redone ESP, load it as a master in the CK, make your changes in your own plug-in file, then revert it back to an ESP header.

You can do this in Wrye Bash.