Wow, I'm having vuja de (that's the weird feeling that none of this has happened before.)
I had a 41.5 bass that was Eb neck. Now I have a 43 that is a D neck. Some say different scales are harder to get used to than the D / Eb issue, but for me, the D / Eb issue was more problematic, and I still sometimes go up to a note at the heel and, well, I'm only a half step off at the most....
What was that "blue note" you grabbed on the turn around there, Powell? That was way kewl!
If I was strictly a jazz player, I might want the Eb neck back. It seemed easier to find the horn key notes because I could reference them all at the heel. For folk tune and rock stuff I had all the most frequent chord fundamentals at the open end. But the long 43 and the D neck have gradually become normal, preferred perhaps.
On the matter of changing the scale length, I have noticed that on my D neck there are also other built in references that would move if I fitted a false nut. The overstand point marks the F, C, G, D, A notes and makes it easier for me to find my way up to thumb position. That would shift if the string was shortened. I'm used to that now, so I don't intend to change anything.
If I liked a particular bass for it's sound and overall response, I don't think either the string length or the Eb / D issue would be considered much.