SoftIndexFileStore may not update index when shutting down

CI has some random failures at https://ci.infinispan.org/job/Infinispan/job/main/450/testReport/junit/org.infinispan.persistence.sifs/SoftIndexFileStoreFunctionalTest/testPreloadStoredAsBinary/

After investigating this is caused by the index not being updated when it is shut down because pending updates make it look like the cache segment has no entries. We need to only update the entries per segment after making sure all updates are applied.