Recently worked on an interesting case. Customer had an existing Merge Replication and it was working fine.
They added a new article to the existing Publication and ran the Snapshot Agent.
Now Every time Merge agent runs we see that Schema changes were getting re-applied.
At the start of a synchronization, the schemaversion of the subscription is checked against sysmergeschemachange by the Merge Agent, and schema changes are applied to the subscriber accordingly.
Ran these queries on the subscriber
select max(schemaversion) from sysmergeschemachange
select schemaversion, pubid, subid from sysmergesubscriptions
schemaversion pubid subid
15 A0B0FAA8-22B9-4CC5-8AED-547F2EBCEB83 85CD9161-5659-42CC-A501-BB43072B0045