Don't worry about it, you'll be fine. I installed a huge pack of themes in a linked emuNAND, and the theme usually reverts to default in sysNAND. But when you're back in emuNAND all you have to do is go into your theme settings and select your theme again and it'll be back to normal. If you picked themes for the shuffle feature, it still remembers what you picked. So it might be a minor annoyance to reselect your theme, but you won't be in danger of bricking your system.
I have a legit theme on my emuNAND now, purchased in emuNAND from the eShop after 9.2 support came out. So it doesn't appear in the themes list in sysNAND, but the theme usually stays active when I go into sysNAND to switch modes. Sometimes it even stays in sysNAND after a hard boot, weirdly. When it switches back to default I just have to pick it again in emuNAND.