The WebLogic JMS File Store cannot be shrunk or decreased in size in any way. There are two primary ways of dealing with this issue
1) The Weblogic Admin Store Utility can be used to compact it. This doesn’t decrease the size of the store, but it does reorder the records within it to allow the reuse of the existing space more freely.
2) Ensure the all the messages have been drained from the store and then delete the store. A new file store will be created on startup