Will doing so re-link the sysnand and emunand?
No
I have seperated sysnand and emunand.
The process I did was.
1)boot sysnand
2)remove 3ds big sd card
3)format system memory
4)did the whole process of setting up 3ds as it was like running for 1st time
5)inserted 3ds big sd card and let it creat homemenu stuff
6)Entered my NNID information on sysnand
After that my emunand doesn't lose theme choices or ask me to unwrap presents every time I booted on it so it is seperated.