I think the dmv knows if the car has a lean on the title. If you previously removed all leans on the title and the title you had (the lost title) was issued only to you, then you should be able to get another one reissued. If the title you had had a lean on it, you have to provide a document from the lien holder that says you satisfied the lien/release the lien. You should check the state dmv site for more information, if you live in texas here's a link http://www.txdmv.gov/motorists/buying-or-selling-a-vehicle/add-remove-lien
Your state's DMV website should have the answer to your question. I know here in CT you just fill out a form to get another title. If you've never received a title before there's another form to fill out in which you basically swear you're the legal owner and that there are no liens on the car. You're not the first person to be in this situation, there are procedures in place to deal with this sort of thing.