Pre installed LUT's gone!

The problems you are experiencing are caused by tampering with the LUTs within the application package - please do not do this - it's not a recommended or supported workflow.  I know there are a lot of very official looking tutorials out there that tell you to do this, but that information is wrong.  The safest way to proceed at this point is to completely reinstall PPro and AME so the LUT directories are restored to their default state as intended by our engineers.  You should then install your custom LUTs according to the directions below.  You will then need to remove all LUTs from your project and reapply them.  I know this is inconvenient, but it really is the safest way to make certain your project will render as intended.

If you are using several custom LUTs and want them to show up in the Lumetri dropdown menus we have a solution which was introduced earlier this year (2018 - version 12.1).  You can install your LUTs into a specific folder in your user library and Lumetri will scan them in. Here are steps to set that up.

Mac

1. From the finder, use the Go menu to navigate to this directory: ~/Library/Application Support/Adobe/Common/
2. Create a folder named LUTs
3. Create two more folders inside the LUTs folder: Technical and Creative
4. Copy technical conversion LUTs (often called camera LUTs) such as LOG to Rec709 into the Technical folder
5. Copy creative LUTs such as day-for-night, B&W, or anything that is just a stylistic look into the Creative folder
6. Restart PPro
7. Technical LUTs show up in the Input LUT dropdown inside the Basic section in Lumetri
8. Creative LUTs show up in the Look dropdown inside the Creative section in Lumetri

Windows equivalent directories:

~\AppData\Roaming\Adobe\Common\LUTs\Technical

~\AppData\Roaming\Adobe\Common\LUTs\Creative

This is a convenient and easy way to add as many LUTs as you like to the Lumetri dropdown menus and this will persist through updates - unless of course you delete or change this directory.

P.S. This is a good example of why not to update any software in the middle of a project, especially in the home-stretch.  I've been there myself.  I feel your pain.  I wish I had better news for you.