I created jobs within each customer and reselected the jobs within paid invoices. The invoices are now categorized as unpaid. How do I fix this?

I don't use Quickbooks so can't tell you, but I would suggest you do backups more often. Every time you do something would be a good time, but if that's getting overly-ridiculous, then at least after you do anything more major (like spending an hour entering a bunch of checks), or before you're going to do something you don't want messed up.