Yes, I observed that the queue operations are sort of ineffective, when working with millions of links. If you wanna fresh start over, you can try to delete the queue manually (with yacy down), by deleting DATA/INDEX/freeworld/QUEUES/CrawlerCoreStacks content and start it up again.
While starting your crawl again, make sure you understand the mechanism how the links are added to queue, especially the filters in Advanced Crawler, as discussed in the documentation and recently in the forum as well.