So I love the sound of an upright's low, thumping end, but I also love the bright, clarity of an electric bass's high strings. So I think the best idea would to put flatwounds on my bass for my E&A and then put roundwounds on for my D&G. I just want to know if this will harm my bass in any way. I was also thinking about doing the opposite for my fretless bass (the first idea is going on my fretted). Any comments/cautions? Thanks!
it wont hurt the bass at all. roundwounds on a fretless wear down the fingerboard after a while
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I dont think that would put your bass at risk or cause any noticeable damage...I've had several different brands and types of strings on my 6 string bass and nothing unusual or bad happened...I had some D'Addario and Ernie Ball Roundwound B, D and G strings, Rotosound Flatwound E and A strings and one taperwound high C string that I bought alone (it was the only string in its package and I could tell it was pretty old, and the package said it was a taperwound string...whatever that is) and nothing bad happened...Except the slap tone was god-awful on the E and A strings...

BTW I didnt choose to have those strings on my bass, they were like that when I bought it used...Except the C string which I bought...

However, putting roundwounds on a fretless is generally a no-no because rounds can damage the fingerboard...
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Roundwounds will wear a fretless fretboard much more quickly. If you want to coat your fretboard to toughen it up, you can do that. Or if you're not afraid of fretboard wear, well, go ahead.

Or you can try groundwounds. I've never actually seen any, but they are supposed to exist. They're roundwounds that have been ground, so they're kind of a flat/round hybrid. Easier on the fretboard, more of the roundwound sound.
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^also called half-rounds (at least on guitar). d'addario makes them for guitar, so i imagine they do it for bass, look on their site. i've played them a little, they're actually ok, give em a shot if you can find them. they aren't perfectly smooth, but close.
well i played a 1969 yamaha bass ... cant remember what model. but it was fretted with flatwounds. the sustain was really bad, but i guess that was normal. however i noticed that natural harmonics sounded a hell lot nice with them on.
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^Flatwounds by nature have no sustain, as they originally went on bowed instruments, which got their sustain through a bow.