This issue is discussed in this thread:
http://forums.atlassian.com/thread.jspa?messageID=257246364

However, the bug I'm reporting is because it seems that when an issue is deleted, then the pcounter value should be adjusted. In particular, when all issues for a project are deleted, then the pcounter value should be reset to 0.

I don't see any value in keeping the pcounter for that project at the same number where it was before the issues were deleted.