.jar files in use on a restore

Recently we have run into an issue when trying to run upgrades of our
software. I have a clle program that does a restore to an ifs directory
with new .jar files. There have been instances lately where objects have
not been restored because they are in use. Speaking with our java
programmers I did learn that there was a change made in the past year to
create a connection pool and keep it open for a longer period of time for
performance enhancing reasons. Doing some testing, we removed the
connection and are now sending the data from the rpg programs to the java
methods. We are still finding that the .jar files stay in a "in use" state.
Can anyone tell me how we might get around this or why this seems to be
happening all of a sudden? We even did a simple test adding a classpath of
3 .jar files and running 2 programs, the first opens a connection and prints
and the second closes the connection. Those 3 files still are in use and
unable to run a restore against.