I'm not sure that is an error. It looks more like an information which said it found SODE entries in the XML files on P3D4, so it's going to remove them.
It is quite odd, since under P3D4, SODE should never use the DLL/EXE.XML files to install into, but only the new add-on.xml method. That's why SODE flag it as a warning. Is it possible you installed SODE manually or, even worse, used the dangerous Migration Tool, that installed SODE in the "FSX-way" ?
In any case, did the SODE Platform Manager managed to remove the wrong entries automatically ? You can also run the Platform Manager separately, after the installation.