In our product RE:Flex (in the Morph plugin) one can just animate the Key Pix checkbox along with Auto-Align button checked and you are in business. Unfortunately that does not work in FCS.
With Twixtor you have to twixt the last good and first good frames and then reinsert that… or variations on that theme that implies to in a nested sequence recut by duplicating your layer and by changing the in/out points eliminate the bad frame(s) and then in the parent sequence you reset the proper timing by animating Twixtor Frame value parameter. For example so that if frame 50 of 0 to 99 is bad (was the one removed in the nested sequence), then at frame 0 value 0, at frame 49 value 49, at 51 value 50, at 99 value 98.
Pierre