You have system converted from Lx 4.1 to 4.2 and you are having a lot of problems. Do a fresh install.
Users need to understand that if they do a lot of customizing or installing 3rd party software a distribution upgrade is likely to have problems. Sometimes it is not worth the time and energy to problem solve all this.
Post-edit: Even if a user has data they do not want to lose you can do a shared folder with the host system. Such data should be in a shared folder anyway.