The following applies to BPM Studio 4.0 and above.

The XSDs, under "Service Descriptors" folder, are generated from Business Object Models(BOMs). They can either be generated from a service task definition or exporting BOM to XML Schema. When projects containing such XSDs are imported from an older version, they will be deleted by BPM Studio either on project import or project clean/build.

The reason that the XSDs are being removed is that they contain an annotation stating they were generated from a BOM. The system is tidying them up as it thinks they are a build artifact. Hence if the XSDs contain such an annotation and they are present in the "Service Descriptors" folder they will be deleted. Here is an example of the annotation - 

 <xsd:annotation>
    <xsd:documentation>BOMORIGIN::/abc.xyz/Business Objects/PQR.bom</xsd:documentation>
  </xsd:annotation>

TIBCO Business Studio - BPM Edition v4.0.0 onwards there might be a case when studio deletes an XSD on import and/or on project build

All supported platforms

The workaround is to manually edit these XSDs and remove this annotation. The annotation is at the top of each XSD.