Update: problem solved.
I got this information from Line6 technical support:
Hello,Re-installing the flash memory on the Variax is the only way to get those models back on the Variax guitar.When you re-install the flash memory on the Variax, please make sure that you are selecting 'NO' when it asks if you would like to keep the presets on the Variax.I would try re-installing the flash memory again (a few times more if needed). Also, if the all models return, but are in different locations than where they should be, you can calibrate the guitar following the procedure in the middle of this document: http://line6.com/support/docs/DOC-3857If the problem persists, there may be a hardware problem with the guitar that would need to be serviced: http://line6.com/service_centers/There are limited parts for the original Variax guitars, so if it is a hardware problem, it may need to be repaired on a component level.Regards,Line6Hugo
I had to calibrate the guitar and now I have all the factory presets back.