First thing to do is check (don’t change anything) Tools-Customize-Colors and see if your changes are there. Then check Tools-Customize-Extensions (edit the extensions in question) and see if they still point to the color scheme you intended. In your user config area see below, you will have a Meconfig.db and Meconfig.bak. With ME not running rename the .db file to .old and the .bak file to .db. Restart ME and see if the colors are back. If not stop ME and undo those extension changes.
Couple ways to backup colors. A you can go to Tools-Customize-Import/Export and Select a file name on the top right. Then select color type, then either Cntl-Click on the colors you are interested in or Shift-Click the whole list. Then press the right facing arrow. Then press Export. To restore the colors just do the opposite.
Alternatively in the file Meconfig.db (with ME not running) scroll down till you see Colors.db. Select and copy all the color records below (until you hit the next .db record start. keep that somewhere and you can use that to restore your colors. As a precaution always make a backup of Meconfig.db before making changes.
Your config file location is Location is Users\USER\AppData\Roaming\Multi Edit Software\Multi-Edit\11\Config.04 Substitute your user name for USER
One more thing, when making changes to colors, in Tools-Customize-Colors always hit the save button before you leave the dialog, or your changes only effect that session and will be lost when you exit ME.