PASOE: ABL Apps write to the same agent log file

2 ABL Applications use SOAP requests and each has their own log files but both services are writing to the same log.
ABL Applications are using the same log file even though they are setup to use unique log files
Multiple applications are deployed to separate ABLApps for each WebApp
Unique log files are configured in openedge.properties: localhost-access.yyyy-mm-dd.log shows individual HTTP(S) POST requests for each webapp
access.log clearly state the individual requests were received against the expected endpoints
catalina.yyyy-mm-dd.log  shows the "ProtocolHandler" entries which verify distinct by the HTTP(S) listener ports
[app].agent.yyyy-mm-dd.log shows no activity for one webapp and the other shows it’s request but also some activity from the other apps endpoint

There are also a LOT of unknown "?" entries in all the agent log files:  

To date we haven't managed to unwind enough to indicate an OpenEdge defect but rather that the conflicts which arise are related to how the multiple instances are (incorrectly) set up:
For example:

• "config copying" an instance directory and then manually modifying properties without registering the (instance copy) with pasman register or incorrectly using 'register service' instead
• when deploying the oeabl.war and not specifying the full ABL App and Web app 
• deployment of the PDSOE webapp from an earlier OE version

For example, the strategy of deploying to a PAS instance and moving that whole instance forward to a new OE version is incorrectly used:

• There may have been omissions as the code / instance was promoted forward, for example when oeablSecurity.properties is missing, WebApps were built under a different version of OE for PDSOE, instead of the current version
• Applications may have first been deployed directly and then migrated to be an ABL application deployed into the new consolidated instance. In other words applications were deployed into a PAS instance then copied into the consolidated instance along with manual updates to the openedge.properties file.
• Instances have been deployed to the same oemanager webapp:8811 which is the oepas1 default. Some sites copy “oepas1” to re-purposed it as the base PASOE instance with manual edits, which are then used for other instances

Other indicators:

• instances.[unix | windows] may show entries from {CATALINA_HOME} instead of {CATALINA_BASE} 
• instances not in instances..[unix | windows but are still in pasmgr.properties in DLC\properties or {CATALINA_BASE}
• instances in pasmgr.properties using the same oemanager webapp

Ensure the PASOE instance is properly tailored for the new OE version and contains all of the latest copies of any default WebApps (eg. manager and oemanager).

1. We strongly recommend migrating to OpenEdge 12.2, when a migration has not gone live yet and not carry forward any items from previous versions if this can be avoided.  With 12.2 being a LTS release it is the pragmatic approach for two reasons:
2. To fix this problem: Delete and recreate all PAS OE instances from scratch *in the same version used*.
(irrespective of upgrading to 12.2 or remaining in an earlier version)

a. Create the PAS instance

b. Deploy ABLApps for each WebApp:
eg: ABLApp called “ABLAPP1” and a matching WebApp called “WEBAPP1”, (webApps=webapp1) association Article  Must oeabl.war be deployed multiple times when multiple ABL applications run in a single PASOE instance  
  
c. Create the associated application WebApp .war files in the same version of PDSOE then deploy into the instance.
In this way when deploying the Webapp into the a new ABL application into an existing instance, it will for example include a copy of the correct version's oeablSecurity.properties and similar tailoring will be correct.