Not sure if this is the right board for this, but here I go. I've got physical copies of Sonic 3 and S&K. I had a completed save on the lock-on, but for whatever reason it got wiped along with the saves in S3. The lock-on has a few saves on it that I don't care about at all, but S3 alone has some different saves that I've made some progress on. Is there any way to clear out the saves on the locked-on game so I'd maybe be able to carry over progress from one set to the next or am I just SOL?
Of course it's only a hypothesis, but your FRAM is probably dead. On second thought, I completely misunderstood your question. I am sorry.
If you delete all your S3&K saves from the save screen, and then turn the power off and on, any valid Sonic 3 save files will be imported into S3&K. You have to delete them all though - it won't import if there's any S3&K data saved. Both S3 and S3&K saves are stored on the Sonic 3 cart, so as Nineko says, failing FRAM could easily cause both sets of saves to be erased.
I have nothing worth saving in S3K, good to know there was such a simple solution. You're a savior, Tiddles.