MAGENTO 2 | Theme layout changed after running UPGRADE command

Question

I am currently working on a Custom Magento2 Theme.

What I have done:

1. Copied all of the vendor/magento/module-theme files to my own module (Named Customod)
2. Copied all of the vendor/magento/theme-frontend-blank files to my own theme named TMP
3. Replaced all of the namespaces in all files with my own namespaces
4. and... IT WORKED, so I edited all the template files and started to customize my theme.

THEN...

1. I followed a tutorial. One step was to run the Magento Upgrade Command from terminal, so I did...
2. After that, I refreshed the frontend and was shocked to see that my theme was completely changed and everything was not the way I made it! But the strange thing is that all of the files in my module (.XML, .PHTML, .PHP) are not changed!

So my question is:
What does that UPGRADE command do? And how can I go back to the way it was? (Because all my data and structure is still in the .XML files etc.)

Answer 1

After 3 days i have found the answer...

The Upgrade command had changes the order of the Modules in App/etc/config.php

My own module was suddenly on the first index of the array, so my theme was overruled by the magento theme and modules.

I had to move my own module to the last index of the array and it worked...