Have there been writings on what exactly git's migration strategy to a new hash function will be? Apparently they have a seamless transition designed that won't require anyone to update their repositories, which seems like a pretty crazy promise in the absence of details.
In git the SHA-1 hash is simply an identifier for an object - it's used in the filename, but not stored in the object. And when a commit or tree object references others, it's just a name that can be looked up in the database. So a commit object hashed with SHA-256 can easily reference a previous commit that was hashed with SHA-1.
During the switch, a bit of deduplication may be lost. But the only interesting issue I can see is how git fsck will tell which hash an object was created with when verifying the hash (maybe with length?).