You wouldn’t need to relearn theory or reading music. You wouldn’t need to learn to establish a practice regimen. You wouldn’t need to relearn to hear intervals or feel a beat.
Going from flute to guitar, you would need to memorize the positions of notes and chords. You would need to develop calluses. You would have to suffer the pain of learning to contort your hand to make barre chords. It would take a lot of practice to develop the muscle memory you need to play proficiently.
If you’re going between similar instruments—organ to piano, for example—you would certainly be influenced by the techniques of your original instrument. It could be an advantage. Chords are fingered the same on both instruments. But you’d have a set of disadvantages to overcome as well. In this example, you’d have to learn dynamic expression in a whole new way. Suddenly, the force you put on the keys matters in a way it never did before!
The answer definitely depends on what instrument you’re coming from and what instrument you’re going to. But, in general, yes, as an experienced musician, you have a considerable advantage that an absolute beginner lacks.