In the Administrator, when opening BusinessConnect > System Settings > Certificate Store we can see attached (Error.png) error screenshot. In the administrator logs, this error occurs:

<<<<<
Caused by: java.lang.NullPointerException
    at com.tibco.ax.gui.bcwebadmin.consoles.ss.castore.CredentialListAdapter.getCollection(CredentialListAdapter.java:110)
    at com.tibco.ax.gui.bcwebadmin.consoles.ss.castore.CaTableModel.applyFilter(CaTableModel.java:69)
>>>>>

Can’t open BusinessConnect Certificate Store.

All

Perform the query shown below. This will give the identifiers of business entities (transports, etc), plus any missing participants. Please note the query doesn't identify all missing business entities for which a credential item can be associated because a full query would be quite complex, and disclose persistence layer details which should not be disclosed.

SELECT OWNER_OID, CLAZZ FROM BC_KEYSTOREITEM WHERE OWNER_OID NOT LIKE ServerInfo?% AND OWNER_OID NOT LIKE DmzInfo?% AND OWNER_OID NOT IN (SELECT OBJOID FROM BC_PARTICIPANT); 

Please note: ServerInfo?% and DmzInfo?% should be wrapped in single quotes when executed on the database.

No database backup is required as this is a select operation.

The result of this query returns records of credential entities owned by participants that do not exist in system (orphan records). 
Make a backup of bc_keystoreitem table data and delete these records. This should solve the problem.