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Trains in France are complicated with bikes... trying to get a proper answer from SNCF about availability is a pain in the arse.
Nightjet say this:
You can take your bicycle along on the following routes:
NJ 490 / 491 Vienna - Hamburg (3 bicycle parking spaces)
NJ 40420 / 40491 Innsbruck - Hamburg (3 bicycle parking spaces)
NJ 464 / 465 Graz - Zürich (3 bicycle parking spaces)
NJ 470 / 471 Zürich - Hamburg (3 bicycle parking spaces)
NJ 466 / 467 Vienna - Zurich (3 bicycle parking spaces)
NJ 408 / 409 Zurich - Berlin (3 bicycle parking spaces)
NJ 402 / NJ 403 Zurich - Amsterdam (13 bicycle spaces bookable in IC
60402 / IC 60403, Bookable at an SBB or NS ticket counter)
As ever, the weak link is Eurostar. Still need to box for that. But not sure if you can take boxed bikes on Nightjet (OBB sleeper).
I've seriously looked into getting a Rinko-style bag and taking the forks out to package it up in a cube. At that point it is just a big bag and can go on any train.