Workaround:
1). Open the securityPolicyAssociation file in a text editor and manually add the missing namespace in BWSharedResource tag. For the example discussed earlier, you will have the following XML for Security Policy Association.
>>>>>>>>>>>>>>>>>>>>>>>>
<BWSharedResource xmlns:inLine="http://www.WSDLNamespace.com/" xmlns:ns10="http://www.WSDLNamespace.com/">
<name>SecurityPolicyAssociationAPI1</name>
<resourceType>ws.security.policy.association.resource</resourceType>
<config>
<applyTo>/Processes/SubProcesses/GetRSNURL.process/SOAPWMSIReqReply</applyTo>
<systemSecuritySubject>/Processes/SubProcesses/GetRSNURL.process/Wmsi.Services.LoginService/RecordKeeperLogon</systemSecuritySubject>
<inbound>
<selectSignatureParts/>
<selectEncryptionParts/>
</inbound>
<outbound>
<selectSignatureParts>headers/Header.To/ns10:To</selectSignatureParts>
<selectEncryptionParts/>
</outbound>
<outboundMessagePolicy>/SharedResources/Security/Policies/SecurityPolicyOutboundAPI1.securityPolicy</outboundMessagePolicy>
<inboundMessagePolicy/>
</config>
</BWSharedResource>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2). Save the file and refresh the project. You can also close and open the Designer project.