Could additionally be the by-product of doing a hurried setup:
In just over two weeks the Company has staffed and equipped a fully functional laboratory and is now in the process of developing the next generation of spider silk products. Consistent with the Company’s Ethos of efficiency and frugality, the lab was finished ahead of schedule, and under budget.
If that is the case it isn't really starting from scratch. As Jazz stated that is why they have frozen eggs. They can purge the entire crop and hatch a new batch.
But this is why I am not sure it's as simple as wandering worms but I am in no way qualified to judge.
My opinion is that it wouldn't take "quarters" to fix if it was just a restart. But I do agree the fix is already implemented.
JMO My sceptical side says that this problem was the cause if the issues with the past reelers. Set up the reelers fiber tension on a strong cocoon and when a weaker fiber is processed the fiber breaks.