To update existing enterprise application we do not have to stop the application since WAS stops the application before updating the code .
Based on the update you gave i am assuming this is a network deployment manager setup , so possibly problem is with sync is not taking place after updating the app and save .
Are you explicitly invoking sync operation after application update ? If not , i would recommend that.
Still problem persists then most likely for what ever reason nodeagent process is not invoking app expansion into installedApps folder but you can take a quick look at nodeagent systemout.log file or ffdc files to see if there is any clue about expansion process.
As a work-around you can also use EARExapnder.sh/bat tool available /profile_home/bin directory to expand the application into installedApps when the app is really updated in config/cells/cell_name/applications but not under installedApps folder.
I hope this helps. Thanks VT These opinions are my own.