I'm going to start the process of chapter 13, and do a lien stripping of my second.
I just found out that through the title search, they never recorded a lien on the title. What can I do about this second mortgage?

A mortgage, when properly recorded, is a lien. If they never recorded it, they don't have a lien to be stripped.

List the debt, in your bankruptcy schedules, as unsecured. If they want to claim that they have recorded it, they will have to prove it.