O3DS or N3DS?
For O3DS you can either restore your NANDmin.bin if you want to keep everything or just update if you don't mind losing everything.
For a N3DS you HAVE TO restore using the NANDmin.bin you made before the ctrtransfer. If not you'll have to jump through some hoops(ctrtransfer to 9.2.0, then update normally, then have to fix DS.DSi mode since ctrtransfer breaks that).