Avoid schema mismatch in System-Versioned tables
Just in case someone faced the same issue:
The fix is to go to [YourDatabaseProject]/bin/Debug folder and clear it and then build without removing anything.
Hope this helps!
We just experienced this issue. We found a workaround by commenting out the system versioning elements of the table (effectively making it a normal table), building the project with the schema change we needed (which succeeds), and then putting the system versioning lines back in place (which also succeeds).
I can reproduce this problem. We (the SQL Server tools team) will work to get this fixed in a future version of SSDT. In the meantime, I believe you can work around this by explicitly defining the history table (i.e. add the history table with its desired schema to the project), and then manually keep the schema of the current and history table in sync.
If you encounter problems with explicitly defining the history table, try closing Visual Studio, deleting the DBMDL file in the project root, and then re-opening the project.