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SCA not including filegroups


Running with the following environment 
Windows 10 (1809 17758.4)
SQL 2012 (11.0.6607.3)
Visual Studio 2017 (15.9.3)
SCA 3.0.18331.2906

I'm evaluating SQL Change Automation for a possible change from our current tool (SSDT).

I've updated the sqlproj file and have the option

However when I'm refreshing I'm getting an error
Creating [Cougar].[BudgetFile]
Msg 1921, Level 16, State 3, Server KFA500009\SQL2012, Line 1
Invalid filegroup 'CougarBudgetFilesFG' specified.

I've noticed that the Shadow database that's created doesn't have all the files and filegroups from the source database. I've added the missing files and filegroups, but they go missing again.



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