Similarly I don't think you could just import a Doom level to a Duke3D level without losing something. Of course on the one hand we have the different weapon and enemy types that can't just be copied. On the other we have the different capabilities of the engines. Doom's engine is more primitive than Duke3D's, since Duke has the ability to put spaces above or below other spaces with some trickery, while it's not possible to do so in Doom. Duke levels will generally feel more lifelike and realistic (cityscapes, alien bases, etc) while Doom's will feel more abstract. Porting maps between the two games wouldn't work that well just because of the different theme and atmosphere they go for. Theme influences level design just as much as systems do.
If we consider the aesthetics, yes things become harder (although Blood could be a bit closer) but i was focusing on the mechanical side (since the topic is level design) and especially on the Doom to Duke direction (not the other way around) as i actually remember Ken Silverman had written a tool to do that sort of conversion (the Build engine can represent all of Doom's spaces, again ignoring aesthetics - that is, textures). However even though they do not work the exact same way, Doom has monsters that could be substituted with Duke's monsters (e.g. zombieman -> assault trooper, shotgunner -> pigcop, imp -> octabrain, cacodemon -> assault commander, etc) and similarly with weapons (i think only chainsaw doesn't have an equivalent) and powerups.
Of course adjustments will need to be made, as you mentioned, but i think they'd be much easier compared to a Thief-to-Dishonored, since the Doom and Duke play much closer to each other, to the point where most of the work can be even automated (like the program Ken Silverman wrote, although with the added ability to do entity and art substitution) with only manual fixes applied to the generated Duke map file - mainly for adjusting difficulty and fixing collision issues that might occur from the enemy placement.