is it possible to override the Templates in the Groupjive Plugin?
Yes, make a new folder at the following location.
/components/com_comprofiler/plugin/user/plug_cbgroupjive/templates
For example "custom" would give you the following.
/components/com_comprofiler/plugin/user/plug_cbgroupjive/templates/custom
Now copy over any files you want to modify from "default" to "custom". Next within GJ select "custom" as the template. You can now freely modify the files you've copied over and have them take affect.
Will the Changes be kept after software update (we afraid that our changes could be lost)?
As long as you use a custom template your changes will be safe. If however you modify the defaults you will lose your changes on update.