Hello Sridhar,
From the error it appears more to be a structure mismatch. Please check the XML that you are receiving in that port and try to import that XML manually. Make sure that the XML is generated according to the new XSD structure.
The error: There are multiple root elements defined in the xml schema. states that the XML schema has more than one root element in contrast to one root element that you would have used for mapping. If everything is fine, please restart your import server alone once and check, it should work.
Post us with your result.
Kind Regards,
Thamizharasi N