When I modify a theme, then import it, an entry is added to the list of themes. If I make another change to the same theme and import again, another entry is created - instead of overwriting the existing them. I can’t be the only person who has noticed - can I?
No, you are not and to my knowledge, there is no way around it. I just make a habit of deleting the old theme (usually before I import the replacement).
Well there is that! So I guess I should be happy there is a workaround!
It just seems like such a huge oversight :-(
“Theme Management” - how hard could that be really? Or at least a “Delete Theme” option next to the Import button???
As a software developer for over three decades, I would consider the whole theme feature to be incomplete and as such would never allow it in a commercial app. Then again, I’m a dinosaur from the old days before being a geek was cool 
But if this is the kind of attention to detail I can expect with this app, then I am probably better off not investing more time evaluating it and should just stick with the horrendous GMail!
Just IMHO, I have tried virtually every email client there is and I find eM Client easily the best. They all have strengths and weaknesses, but in this case the strengths far outweigh the weaknesses.
A way to avoid the duplication of your theme by import, is to paste the theme file directly to C:\Users[username]\AppData\Roaming\eM Client\Themes, replacing the existing file. The only issue with that is that you need to restart eM Client for the changes to be recognized.