Quicken has gone back over transactions over roughly the past year and "unsplit" them all. Best I can tell, they are now all categorized as 100% from one of the categories in the original split, I think the last one, but I can't be sure.
This is incredibly frustrating. For example, in my paychecks I get a reimbursement for my home internet access. So, I split those deposits between my wages and home internet. Now those transactions for the past year just say one of the those categories. And, all of my mortgage payments that get split between paying my mortgage, my escrow account, etc. are just in one category.
I'm guessing there's nothing I can do about this other than spend 10+ hours manually fixing everything for the past year.