Considering nulled themes tend to cause problems down the line (viruses, hacks, etc.), I would rebuild the site with the clean theme on a completely different server.
There is no problem, bro. Just upload the new file rar file from your legit source, and replace the old one. If you have bought a legit theme, they will offer you support for some time. Use that time to solve any issues that may arise from the changes.
I'm currently running a nulled theme but want to buy the legit license.
If I deregister the code and add my legit one, there should be no problem? Or will I have to completely remove the theme file and upload a legit file?
To be honest, I'm happy to see that you have decide to support the theme developer.
Now.. you said that you have solve it.. I hope that you did content migration and not file overwrite just to be sure that there are no funny scripts left from the nulled one.