Looks like you're using HSQLDB, so your database files will be in that directory, and you don't want to delete those.
A good method is to build the new bundle, stop the server, delete all the old versions of the same bundle files that you just generated, then copy in the new files, and then start the server. Just make sure that the server is fully stopped before swapping files to make sure it doesn't still have a handle on the old ones. You should end up replacing/regenerating all the *.obj files. Also make sure you're using 1.1.14 to generate the bundle:
Do you know where your GTFS-realtime feed is?
Your onebusaway-transit-data-federation-webapp data-sources.xml should be pointing to it. Or another type of real-time feed API.
If you can see the server log, you should be getting messages such as "X of Y trips matched", and if no real-time info is matching then X is probably 0, or very low. Essentially, the trip_ids in your GTFS-realtime feed need to match those in your GTFS trips.txt file. Typically these IDs change every time the schedule/GTFS data changes. If those IDs don't match, you won't see any real-time info in OBA.