After merging a lot of partitions (from 1001 to 200) and removing all unused files and filegroups, I ended up with "incosistent metadata" on a partitioned table. Luckily this was a test database, to test the partition merge.
select * from dbo.Test where CustomerID < 199:
(0 row(s) affected)
select * from dbo.Test where CustomerID > 199:
Msg 606, Level 21, State 1, Line 1
Metadata inconsistency. Filegroup id 15 specified for table 'dbo.Test' does not exist. Run DBCC CHECKDB or CHECKCATALOG.
Every CustomerID is on it's own filegroup: 0 - 199, filegroups fg_00 - fg_199
Apart from this database inconsistency checkdb is not raising an error!
dbcc checkdb() with all_errormsgs
DBCC results for 'MDB_NET_PartitionTestSOV'.
There are 0 rows in 0 pages for object "sys.syssoftobjrefs".
Unable to process index pk_Test of table Test because filegroup (FileGroup ID 15) is invalid.
CHECKDB found 0 allocation errors and 0 consistency errors in database 'MDB_NET_PartitionTestSOV'.
DBCC execution completed. If DBCC printed error messages, contact your system administrator.
To my opinion an invalid filegroup must be an allocation error, or a consistency error, but is not raised as one!