Hopefully, but nothing is guaranteed. The Devs hope to keep things compatible, but it simply may not work out that way, that's all part of Early Access.
If you are not okay with potentially losing all progress/saved being incompatible with future content, you should completely avoid Early Access games.

(And Raft btw could have changes to building that could render your raft incompatible with future builds, for example those who choose to exploit the no support bug with triangle pieces.)