right good point.
The locking was designed for just two scenarios:
1) single application: no locking problems
2) cluster of 2 JVMs on same machine sharing a directory (some people like this setup): no application owns the lock for a long time period.
Still in your scenario, or even occasionally in case 2 as Lucene doesn't guarantee fairness (just polls), this is an issue.
As a workaround until this is fixed (patches are always welcome), couldn't you share the IndexWriter? you would need to join the code of the other project in same JVM.
I'll open an issue linked to
http://opensource.atlassian.com/projects/hibernate/browse/HSEARCH-382