Yes, create a dummy code for the duplicate teacher record and untick them as a teacher. Make sure the codes in Nova-T and SIMS .net match, transfer the timetable from Nova to SQL and re-apply the timetable in SIMS .net
I would suggest you make plenty of backups (in System Manager and Nova) however if you have a call logged, I would leave it to them to talk you through it/do it for you. Also if you are a Lesson Monitor school, you should do all of this work outside of school hours to make sure no marks are lost.