If I actually knew what condition he had, I could have a crack at it - but due to the obscurity of it after a quick run through google, I can't tell what he suffered from. So many chronic back conditions.
Edit: OK, it sounds as if he has Spondylolisthesis going by what some Dortmund fans have been saying. The prognosis/severity of it really depends on what actually caused it, as it could be secondary to another bone condition, like athritis, or it could have been caused by a simple fracture. Admittedly, I'm not big on such orthopaedic/rheumatological conditions such as this - it's quite rare, apparently more common in kids. But it sounds as if Gundogan must have had quite a severe type due to needing surgery.
The fact he's playing again, and doesn't seem to have suffered a relapse since his surgery (a quick read about the surgery itself, it's quite intense - some don't actually help the condition at all, in fact may even make the symptoms worse), is a good sign.