I'm working on building a database in the same space as InstantDB. Currently, it's an "object/graph database using Protobuf". There's a check to ensure updated Protobuf definitions are backwards-compatible. Of course, this still implicitly relies on using Protobufs correctly (i.e. a missing value is the same as zero/empty/null/nil), even though I'm trying to make it safe by default.

I'm curious what your needs are. Would you mind elaborating on what kind of migrations your project would have needed to not die?