You probably had a corrupted DLL.XML or EXE.XML file so, the installer replaced it with corrected one.
In the %APPDATA%\Microsoft\FSX folder, you should find a file named:
DLL_XML_Before_Addon_Manager.XML file. It would be useful if you post it here (use "Attach", don't copy&paste it into a message), so we can have an idea why your file was wrong before installing Geneva.
If, instead, your modules were using the EXE.XML instead of the DLL.XML, the same is valid with a similarly named EXE_XML_Before_Addon_Manager.XML file in the same location.
It might be useful if you also attach your *current* DLL.XML and EXE.XML files