You hashed password entries also have formatting information in them.
"$id$salt$encrypted", where "$id" is the hashing algorithm used (On GNU/Linux, "$1$" stands for MD5, "$2$" is Blowfish, "$5$" is SHA-256 and "$6$" is SHA-512, crypt(3) manpage, other Unix may have different values, like NetBSD).
If your users' passwords have a time-based expiry, they'll eventually have to update them and the new hash will be in the format you've chosen. The system can tell which format passwords hashes are in per user, so things will keep working as passwords are updated over time.
As it also says in the answer you reference:
Passwords that are updated after these modifications are made will be hased using blowfish, exising shadow passwords are not modified