Jet engines will still be fueled by JetA1 or similar - although at some point it will be economical to synthesize it from tar sands, biomass, who knows? The point is that existing engines will keep running.
Then, at some later time, we'll have a breakthrough in either methane or hydrogen production, and new engine designs will show up to use these fuels.
(Didn't Herr von Ohain run his first bench tests using hydrogen fuel IIRC?)
BTW - gaseous fuels like H2 or CH4 are very easy to burn, and first-generation turbines would probably change very little except for the larger fuel plumbing. As later designs are optimized, the combustor (and thus the overall engine length) gets shorter and lighter.
The aeroplanes will then have to change a LOT because fuel density is very low, so the volume required is LARGE. I saw one proposal for a 747-based H2 machine (this was in the 73-74 aero magazines); the upper deck was extended full length and much enlarged in cross-section, and was one huge SuperGuppy-like H2 tank.
