For one customer I found an application (happened to be RELM) simply wasn't starting.

RELM was not mentioned in any Liberty logs (messages.log, console.log, trace.log).


This warning is expected if relm is listed in application.xml but relm.war does not exist:
[8/24/16 11:12:20:145 CEST] 00000070 com.ibm.ws.app.manager.AppMessageHelper W CWWKZ0014W: The application relm could not be started as it could not be found at location C:/Program Files/IBM/JTS-CCM-keys-Win64_6.0.2/server/liberty/servers/clm/apps/relm.war.

This message is expected if relm.war exists and relm is listed in
application.log:
[8/24/16 11:12:20:145 CEST] 0000006c com.ibm.ws.app.manager.AppMessageHelper                      I CWWKZ0018I: Starting application relm.

The two above messages are mutually exclusive if relm is listed in
application.xml.

Customer's application.xml was last edited in July , and RELM last worked last week, yet there is no mention of relm in the latest logs.

We can rule out that relm is not mentioned in the customer's application.xml, so instead there must be an error that prevents either CWWKZ0018I or CWWKZ0014W from showing for RELM.

I have tried running the max log level on my end by specifying the following in server.xml, but there is no more verbose information that seems relevant:
    <logging hideMessage="SRVE9967W" traceSpecification="*=finest" consoleLogLevel="INFO">

Trace.log rolls over with only one file even though I have specified this:
com.ibm.ws.logging.max.files=100 com.ibm.ws.logging.max.file.size=1000
or
com.ibm.ws.logging.max.files="100" com.ibm.ws.logging.max.file.size="1000"

A colleague found a PMR where --clean was recommended for a similar problem with DM (not RELM).

This solution was accepted:

RELM does not start yet there is no error even though we know RELM is mentioned in your application.xml. The most likely cause of this error is a problem with your Websphere Liberty cache. Perhaps this is ultimately due to the native out of memory errors.
                                                         
To resolve this problem, try to clean the Liberty cache following these steps:                                                                 
(1) Stop WAS Liberty server.                                           
(2) Backup "liberty.server.bat"                                        
(3) Edit "liberty.server.bat"                                          
- liberty.server.bat is at <jtshome>/server                            
- find this line in liberty.server.bat and add "--clean"               
  call "%CLM_LIBERTY_HOME%"\bin\server.bat "%1" %CLM_LIBERTY_SERVER_NAME%                                 
Producing:
  call "%CLM_LIBERTY_HOME%"\bin\server.bat "%1" %CLM_LIBERTY_SERVER_NAME% --clean

On Linux this is the line in "liberty.server":
$CLM_LIBERTY_HOME/bin/server $1 $CLM_LIBERTY_SERVER_NAME;

(4) Start WAS Liberty server using "server.startup.bat"                
(5) Replace "liberty.server.bat" with backup file you took at (2)      

This resolved the issue and RELM would again start.