WSO2 API Manager 2.1 upgrade to 2.6 - wso2-api-manager

Question

We've upgraded our WSO2 API Manager from version 2.1 to 2.6. We are using all in one deployment. After migration we have a very confusing situation. In a Store I see no published API's until I log in to the Store. Then, in a Publisher app I see all the API's in a published state, but when I edit any of them I am not able to save it or go to Implement or Manage tab - always a 'null' error appears. A stack trace from wso2carbon.log for such cases is below. I have no idea what is going wrong and any help would be very appreciated.
TID: [-1234] [] [2019-03-07 09:27:49,622] ERROR {JAGGERY.site.blocks.item-design.ajax.add:jag} - org.mozilla.javascript.WrappedException: Wrapped java.lang.NullPointerException (/publisher/modules/api/add.jag#134)
at org.mozilla.javascript.Context.throwAsScriptRuntimeEx(Context.java:1754)
at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:148)
at org.mozilla.javascript.FunctionObject.call(FunctionObject.java:386)
at org.mozilla.javascript.optimizer.OptRuntime.call1(OptRuntime.java:32)
at org.jaggeryjs.rhino.publisher.modules.api.c3._c_anonymous_6(/publisher/modules/api/add.jag:134)
at org.jaggeryjs.rhino.publisher.modules.api.c3.call(/publisher/modules/api/add.jag)
at org.mozilla.javascript.ScriptRuntime.applyOrCall(ScriptRuntime.java:2430)
at org.mozilla.javascript.BaseFunction.execIdCall(BaseFunction.java:269)
at org.mozilla.javascript.IdFunctionObject.call(IdFunctionObject.java:97)
at org.mozilla.javascript.optimizer.OptRuntime.call2(OptRuntime.java:42)
at org.jaggeryjs.rhino.publisher.modules.api.c0._c_anonymous_43(/publisher/modules/api/module.jag:136)
at org.jaggeryjs.rhino.publisher.modules.api.c0.call(/publisher/modules/api/module.jag)
at org.mozilla.javascript.optimizer.OptRuntime.call1(OptRuntime.java:32)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0._c_anonymous_5(/publisher/site/blocks/item-design/ajax/add.jag:520)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0.call(/publisher/site/blocks/item-design/ajax/add.jag)
at org.mozilla.javascript.optimizer.OptRuntime.call0(OptRuntime.java:23)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0._c_script_0(/publisher/site/blocks/item-design/ajax/add.jag:54)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0.call(/publisher/site/blocks/item-design/ajax/add.jag)
at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:394)
at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:3091)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0.call(/publisher/site/blocks/item-design/ajax/add.jag)
at org.jaggeryjs.rhino.publisher.site.blocks.item_design.ajax.c0.exec(/publisher/site/blocks/item-design/ajax/add.jag)
at org.jaggeryjs.scriptengine.engine.RhinoEngine.execScript(RhinoEngine.java:567)
at org.jaggeryjs.scriptengine.engine.RhinoEngine.exec(RhinoEngine.java:273)
at org.jaggeryjs.jaggery.core.manager.WebAppManager.exec(WebAppManager.java:588)
at org.jaggeryjs.jaggery.core.manager.WebAppManager.execute(WebAppManager.java:508)
at org.jaggeryjs.jaggery.core.JaggeryServlet.doPost(JaggeryServlet.java:29)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:743)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:485)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:377)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:337)
at org.jaggeryjs.jaggery.core.JaggeryFilter.doFilter(JaggeryFilter.java:21)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.wso2.carbon.ui.filters.cache.ContentTypeBasedCachePreventionFilter.doFilter(ContentTypeBasedCachePreventionFilter.java:53)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.filters.HttpHeaderSecurityFilter.doFilter(HttpHeaderSecurityFilter.java:124)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:498)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.wso2.carbon.identity.context.rewrite.valve.TenantContextRewriteValve.invoke(TenantContextRewriteValve.java:80)
at org.wso2.carbon.identity.authz.valve.AuthorizationValve.invoke(AuthorizationValve.java:91)
at org.wso2.carbon.identity.auth.valve.AuthenticationValve.invoke(AuthenticationValve.java:65)
at org.wso2.carbon.tomcat.ext.valves.CompositeValve.continueInvocation(CompositeValve.java:99)
at org.wso2.carbon.tomcat.ext.valves.CarbonTomcatValve$1.invoke(CarbonTomcatValve.java:47)
at org.wso2.carbon.webapp.mgt.TenantLazyLoaderValve.invoke(TenantLazyLoaderValve.java:57)
at org.wso2.carbon.event.receiver.core.internal.tenantmgt.TenantLazyLoaderValve.invoke(TenantLazyLoaderValve.java:48)
at org.wso2.carbon.tomcat.ext.valves.TomcatValveContainer.invokeValves(TomcatValveContainer.java:47)
at org.wso2.carbon.tomcat.ext.valves.CompositeValve.invoke(CompositeValve.java:62)
at org.wso2.carbon.tomcat.ext.valves.CarbonStuckThreadDetectionValve.invoke(CarbonStuckThreadDetectionValve.java:159)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
at org.wso2.carbon.tomcat.ext.valves.CarbonContextCreatorValve.invoke(CarbonContextCreatorValve.java:57)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1775)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1734)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NullPointerException
at org.wso2.carbon.apimgt.impl.APIProviderImpl.updateAPI(APIProviderImpl.java:943)
at org.wso2.carbon.apimgt.impl.UserAwareAPIProvider.manageAPI(UserAwareAPIProvider.java:116)
at org.wso2.carbon.apimgt.hostobjects.APIProviderHostObject.saveAPI(APIProviderHostObject.java:1159)
at org.wso2.carbon.apimgt.hostobjects.APIProviderHostObject.jsFunction_updateAPIDesign(APIProviderHostObject.java:991)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.mozilla.javascript.MemberBox.invoke(MemberBox.java:126)
... 69 more
{JAGGERY.site.blocks.item-design.ajax.add:jag}