Hi,
the Antimatter-theme is separated from the core, i.e. you can download it here http://getgrav.org/downloads/themes . Thus, you can update the core without loss of your changes. I don't use GPM, but at least it should ask and show, which themes/plugins it will update. If you want be sure, just wait till @rhukster or others are repsonding.
However, if you update Antimatter your changes will be lost! To circumvent this you can rename the folder of your customized Antimatter theme into e.g. Matter and change the theme in user/config/system.yaml to
and do the update. If you want to take advantage of the changes in the Antimatter theme, the best procedure is to collect all your changes you have made and create your own theme using Theme inheritance technique described in http://getgrav.org/blog/theme-development-with-inheritance .