Well, it certainly won't be easy, but I think it'll be easier than starting as a complete beginner.
For starters, you'll know the musical side of things. Everyone who's played an instrument knows music theory to some extent, and even if you just know what notes are in a scale, you'll have an advantage over a complete beginner. Any music theory knowledge will help one understand more what one is learning. It may seem like there's a longer way to go because you know from learning one instrument what it takes to learn another, but you're closer than you think, and closer than beginners.
For some instruments, there is a bit of correlation in the actual playing. I imagine most keyboard instruments share similar technique and ergonomics, and instruments of the same family are similar to play (like saxophones). I wouldn't count on much of it for flute and guitar, though, besides maybe the fingering aspect being similar.
I play a couple instruments (decently), and I think the most important thing to remember is that each instrument is different, and serves a different role. Keyboard instruments, like piano, can certainly be melodic, but flute is nearly always carrying the melody, and guitarists need to be able to create harmony in a way that flautists don't usually need to learn.
Best of luck in this endeavor!