in case of MERGE replication:

if it is a matter of schema changes, then perhaps the upgrade should be made in a diferent way, depending on the sql version:

-- in 2000 speciall stored porcedures should be called for the new schema to be applied

-- in 2005, "alter column" statments can also be replicated if you run the script on the publisher.

in both cases new tables should be added as new articles to the publication.

breaking replication and re-initialzing would be nice to avoid, specially for big db's and slow unstable netwroks. it could take hours to re-initialize

what you really need to take care off before you begin upgrading, is to make sure the application users are not using the application and that every data is merged in the publisher.

in this case you dont have any fear of loosing any data in case you need to re-intialize.

give more info on your case.