Hi Kristof,
We had similar issues in our first attempt to upgrade from BI 4.0 SP2 to BI 4.1 SP4.
You could check if the following files sqlrule.llr and sqlrule.dfa exist in <BI_install_folder>\SAP BusinessObjects\SAP BusinessObjects Enterprise XI 4.0\win64_x64
The issue is described in OSS note 2054800
Do not get confused by the description of the note. Just check the files if they are there and if not, copy them from working environment.
There is also an OSS note for FWM 20030. Maybe worth checking it as well. 1924430
Regards,
Asen