Martijndort use you the V11 or V12?
With V11 I had to restore a Database with German special characters and this worked like a charm. The tables was all UTF-8mb3_general_ci. When you restored it with latin1 it can loose the ß, because this is official in latin1 not implemented. latin1_german use the Windows 1252 charset where the ß is included. Also latin15 includes the ß.
If this is the reason, there are programs to convert the charset or you can maybe just change the SQL.