So I estimated a job for a new client. 3 concepts, 1 logo, 1 revision. I gave them 4 to get a feel for their style. They liked none and drew their own. I executed that one plus another original concept that I hoped they'd go for. They like both and want both. How do I re-estimate this job if I got the second logo through my work for the first one?
You already went one logo concept beyond what you agreed to. You should have specified that was out of scope and told them you were billing accordingly. A fourth logo is not a "revision" of the existing three.
Now you've gone two concepts out of scope, plus you're developing the client-supplied logo. Bill hourly (or whatever your contract says) for the development of the fifth logo and for the development of the client-supplied logo.
(As Scott commented, I'm not sure how one company can have two logos, but assuming that's the case...) From that milestone (two approved logos), whatever other work you are doing on your logo (stationery? corporate branding?) is in scope, and the same work on the client logo is out of scope and billed accordingly.
Sounds you've already done 6 concepts? You'd need to be more specific on what you qualify as each and what they qualify as each. In the clients eyes maybe you haven't even done the logo and revision yet, which would mean even more work could be coming down the pipeline for you.
It really depends on client relations and what kind of paperwork you've signed already. It's best to quote a bit of a buffer for yourself, because most clients want the world for pennies, so it's best to protect yourself. On top of that you should mention in your quotes what happens when you go over scope, whether at that point you negotiate the next sections of work, or just work hourly. You should raise the alarm sooner that you're going over what you quoted. At this point if they like yours and the one they've drawn, I'd stop working and just communicate to them that you've already done the quoted amount of work, and you'll be charging hourly to finish the job.
You should brace for the possibility that they'll baulk at your request for more money, because many clients do, and you should be prepared to either put your foot down to bill hourly, or have a compromise in the back of your head ready, like if you think it'll take 5 hours, give them a deal for 3 hours or similar. Really depends on what the client is like.