Hi Arsenije,
You should never need to add hundreds of control points, just a few dispersed through the problematic area should work. Would you mind uploading your recon to our file drop site and I'll take a look at it? You can send it to my email, eboyd2@nmr.mgh.harvard.edu.
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
Emma