I gave it a try today and found a usability problem.

1. Open Configuration Properties dialog, Display tab.
2. Select any theme (e.g. "EmEditor Standard"), change anything -> new theme "EmEditor Standard (modified)" is created.
3. Select Rename from the ">" button menu, give some different name.
4. The original "EmEditor Standard" theme is also renamed.

From the interface organization I expected, that a copy of the theme was created, and that I renamed it, but it seems that the theme is not changed, and that the new item in the list refers to the same theme (since it returns back when I select Save). I think, something should be done to make it more obvious that "... (modified)" is not the new theme.