Like Mez says, probably your only real option is to delete enough of the track to get create a gap between the ends that's at least 1m or so greater than the shortest possible length of the track segments, so you can then autocomplete the extra space.
When I have this sort of problem (not just with trains but any ride where you build the track), I generally delete the entire troublesome area back to the 1st section of track on 1 side that's longer than the minimum track segment length. I then shorten this piece to the minimum and then rebuild either from there or the other end using only minimum length segments. That way, when I get to the other end, I'll have the gap created when I shortened the longer-than-minimum segment and autocomplete will work.