We are using merge replication to provide some filtered data for our clients. Also we use data-tier applications for deploying latest DB schema, stored procedures, etc for our databases. Somehow it turned out that deployment of DACPAC are breaking replication. It took quite a time to troubleshoot it. The root issue was that DACPAC was dropping replication related triggers (MSmerge_(del\ins\upd)_<guid>) during creation of its owns.
Tell SqlPackage no to drop triggers:
SqlPackage.exe ... /p:DropDmlTriggersNotInSource=False
It is cumbersome to recreate merge replication. I dig into process of merge replication creation - How Merge Replication Initializes Publications and Subscriptions. I played with profiler and cherry-picked that stored procedure sp_MSaddmergetriggers. Run next query to for fix:
use [<database>] exec sp_MSaddmergetriggers @source_table = '<replicated_table1>' exec sp_MSaddmergetriggers @source_table = '<replicated_table2>'
It isn't documented nor supported by Microsoft. But it precisely does what it should.