I was looking for an answer for this everywhere and FINALLY found a solution. When we switched from desktop to online, all our inactive clients changed to active because of the old billable expenses we had been using for tracking costs related to employee hours. (I have no idea if we were supposed to do this differently, but that is what we did and had 1000+ records to change). There is a URL you can use to clear out old billable expenses but I was getting an error that "Something is not right". Thanks to a very patient QBO rep, we identified some inactive accounts we had. We activated the accounts and ran the link again and it WORKED. It hid the old billable expenses and switched most of the inactive clients back to inactive. I still have some cleaning up to do, but this was huge. Here is the link: 

qbo.intuit.com/app/managebillableexpense