Postgres: Missing data after Binary Copy - Is VACUUM FULL required?
To answer myself. 

It was somehow related to  https://www.postgresql.org/message-id/flat/111D0E27-A8F3-4A84-A4E0-B0FB703863DF%40s24.com#111D0E27-A8F3-4A84-A4E0-B0FB703863DF@s24.com i think.

The OS changed from Debian7 to Debian8, and so the dynamically linked libc6 changed. 
Had to do a REINDEX on all my Tables with Indexed String Columns.