I wanted to make custom Character styles to speed up my input time (e.g. formated Greek, Hebrew, Arabic, Akkadian etc.). I created many Character Styles and they were working fine. Upon restart of Nisus I noticed all of my custom styles were gone. I attributed it to the font issue and made a couple of new ones again (Greek, Greek emphatic, Hebrew etc.). I closed Nisus and launched it again: all of the custom Character Styles were gone again.
I found the/a solution: It has to do with each document having its own Character Styles. The remedy then is to make all of these styles, and if you want them to appear in ever document as the default, then save as a template and then choose that template dot as the default document.
I'm leaving this posted in case someone else might need it.