A lot of misinformation has preceded my post.
You don't want smcFan Control for this job. That will only allow you to set minimum fan speeds in different presets. You DO want HDD Fan Control, which will keep the drive fan regulated according to the input it is receiving from the System Management Controller (the SMC), and prevent the drive fan from ramping up to maximum rpms in this situation. In other words, it will keep the fan revs where they should be.
HDDFan Control is not cheap, However, there is a FREE version of HDDFan Control, which should do the job.
http://exirion.net/ssdfanctrl/
And by the way, smcFan Control, used for the purpose of manually regulating the fan speeds to minimum speeds--it's only purpose--where they would not be ramped up properly according to temperature, will NOT prematurely burn out the fan motors, so long as you keep the pre-sets within reason. I have been running smcFan on this Mac for three years plus, with no problems because I know how not to overdo it. But that's for another thread.
But you can't run smcFan and SSDFan concurrently.
And this has nothing to do with resetting the SMC. It's because of the drive replacement.