This is not really a problem. But my wife thinks it’s a problem (uh, oh! I know you’re saying to yourself)… I have a 2007 Mercedes CK550 Cabriolet with a modified engine (modified by Mercedes at the factory just fyi) - giving it 444hp (which has nothing to do with my question, I just enjoy bragging!)… So, here’s my question - I use my paddle shifters all the time - and I mean ALL the time - just like I’d use a gearshift… my lovely spouse tells me that I’m going to ruin the transmission and I should forget the paddle shifters and use the brake at all times… As a compromise (because I’m an obedient husband who does exactly what I’m told), I refrain from utilizing the paddle shifters when my lovely wife is in the vehicle…
So, does using the paddle shifters actually harm the transmission and should I refrain?
I have shifters on both of my vehicles and using them just seems silly in every day driving . As for wear and tear on the transmission all I know is that I can buy a lots of brake pads for what one transmission in a Mercedes would cost .
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Use 'em, that is what they are there for if you choose. They are nothing but switches, the car will prevent you doing something dumb.
Keep the wife happy, let the car shift automatically when she’s in the car and enjoy the flappy paddle shifters when you are alone.
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The car now has 12 years on the transmission, right? And you modified its engine partner beyond the Mercedes’ design specs. But still it works fine. I think you have proven you are right and your wife is wrong. Now tell her she’s right 
OP did not modify the engine, MB did-per post. Maybe an AMG?
The wife is worried about the cost of a transmission in this vehicle and who can blame her . Also it has to be really irritating to ride with someone who thinks they are Formula One driver with all the jerks from using those paddle shifters.