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If you look at the single slice and it still contains all the brain, but just shifted (and it looks like this _might_ be true) then you can try and shift the single slice into place.  To do this you need to separate the image into parts (the section to the left of the single slice, the single slice itself, and the section to the right) - you can do this with fslroi (see the first practical in the FSL course if you are not familiar with this).  Then you can shift the slice appropriately, and then put all the parts back together using fslmerge.

Alternatively, you could generate a replacement slice by averaging the slices on either side of the bad slice.

This would involve taking more parts (separating the single slices to the left and right of the bad slice) and then averaging the single slices with fslmaths, then putting it all back together with fslmerge.

I hope this helps.

All the best,

Mark