I'm using h2db with a test T24 tafj application, I had the same problem but I managed to resolve it by identifying the application that is running h2 (launched when I attempted to setup a database connection).
ps aux|grep java
will give output as:
sysadmin 22755 3.2 0.1 5189724 64008 pts/3 Sl 08:28 0:00 /usr/java/default/bin/java -server -Xmx2048M -XX:MaxPermSize=256M -cp h2-1.3.175.jar:/r14tafj/TAFJ/dbscripts/h2/TAFJFunctions.jar org.h2.tools.Server -tcp -tcpAllowOthers -baseDir /r14tafj/t24/data
now kill this with its process id:
kill -9 22755
and at last remove the lock file:
rm -f dbname.lock.db