Hello Sven,
May I suggest that you try SAP standard report RHCHECKRELATIONS.
This will help you find and fix any invalid entries.
Select Plan Version as Current Plan and leave the object type blank to see all invalid entries.
To be on the safe side, do not select Direct delete on the first screen (leave checkbox blank).
Once the inconsistent entries are displayed, you can select and fix them.
Also since you have a large number of records it might be preferable to run it in the background as it might time out.
Hope this helps.
Warm Regards,
Avanish