Hi Joern,
Are you calling the BO webservices using the consumenr API's provided by Crystal Sever or you directly consume the WSDL?
I am aware there were changes in the web services SDKs, however more of it was related to web intelligence documents.
Refer to the developer guide and API guide for web service SDK's for CR 2011/BI 4.0 from below links and check if you are using any deprecated methods.
Dev guide:
http://help.sap.com/businessobject/product_guides/boexir4/en/xi4_wssdk_dg_en.zip
API guide:
http://help.sap.com/businessobject/product_guides/boexir4/en/xi4_wsjava_apiRef_en.zip
Also, ther is report application server SDKs which you can utilize in case you are not able to use the web services instead of crystal reports for eclipse sdks, as I see that your reports are published to cryatl server which you query using the BO web services to export the reports, thus it makes your reports managed and you cannot open managed crystal reports from CR for eclipse SDKs.
Guides for RAS SDKs are available at
http://help.sap.com/businessobject/product_guides/boexir4/en/xi4_rasjava_dg_en.zip
http://help.sap.com/businessobject/product_guides/boexir4/en/xi4_rasjava_apiRef_en.zip
Let me know if you have any queries after going through the guides.
-Prithvi