We do offer scheduled workflow execution on KNIME Community Hub now, perhaps that’s something your employer could look into 
. The old Batch Execution mode is not being developed any more and may be decommissioned at some point in the future.
Interesting! KNIME (and Eclipse) workspaces are not meant to be used from multiple applications simultaneously, and at least the desktop application does check for that and doesn’t allow you to open two instances with the same workspace. It looks like the Batch Executor application is missing that check, which made your usage pattern possible until now.
The new version of the integrated web browser (CEF) shipped with AP 5.5.0 now relies on the assumption that it has exclusive access to the workspace and crashes during start-up if it doesn’t. While this clearly breaks some (exotic?) use cases, I’d be hesitant to call it a clear bug in CEF. You could also argue that the Batch Executor is buggy because it doesn’t lock its workspace properly. A fix there would also break your setup. I’ll discuss the problem internally and open a ticket.
If you want to continue to run multiple Batch Executor processes in parallel in 5.5.0, you’ll have to assign them to separate workspaces. You can do this using the -data <WorkspaceDir> commandline parameter. You’ll need to write the creation and cleanup logic yourself, but at least it will work. Debugging etc. will obviously be less convenient.
Hope that helps, Leo