"No, it does not come here, but it flies here."
Translation:Nem, nem idejön, hanem iderepül.
Yes, another issue is at play here. The emphasis! The emphasis is on the verbs. Not verb A but verb B is what the sentence says. When the verb is in focus, it does not get split, it stays intact. Compare it with "Nem ide repülök, hanem oda". Not "to here" but "to there" - the emphasis is on the location.
Well, the whole verb, together with the preverb, is emphasized. But you are correct, since the preverbs are the same, the distinction is on the verb root. But we have to be careful with the splitting, since the meaning of the sentence can change.
The easiest way is leaving everything intact but stressing the verb root when speaking the sentence:
" ... nem ideJÖN, hanem ideREPÜL."
Another way is to drop the preverbs completely:
" ... nem jön, hanem repül."
Now comes splitting. It is a problem. Because if we split but leave the preverbs in the same position, then it becomes
" ... nem ide ... , hanem ide ... "
If we split the verbs and put the preverbs behind the verbs, then the sentence changes again. Instead of a specific negation and contrast, it becomes more like two independent statements, one positive, one negative, not really contrasting one another.
So, there is one (or two) more thing we can do. Split the verb, and extract the preverb, placing it outside the active zone, on neutral territory. Either in front or in the back:
" ... ide nem jön, hanem repül."
" ... nem jön, hanem repül ide."
These are more or less equivalent with the unsplit version.