TOPIC:

In case of an update of JEM the default css-files will also be updated so any changes you've made in those files will be gone so better make a backup.

Luckily there are ways to use files that won't be overwritten.

Template override
It is possible to copy a css and place it in: templates/*currentemplate*/css/com_jem/ in that file you can make adjustements.

settings-view
In JEM 1.9.7 there will be an option where you can select a location for the custom-css. Ofcourse don't point to the default location. just to note: when a custom file is active the file in template or media folder won't be active.