I have had structured swim workouts become messed up before, but I always thought it was my own error (despite my usually being pretty attentive to detail).
However, this was the first time that I was able to prove that it was not me! This has been happening every so often for as long as I can remember. Hope it can be fixed soon.
Also, if it matters, the rest interval that was disappearing when I would hit save would end up at the end of the repeat.
This also happened back when I had a forerunner 935, but obviously that should not matter because it is an issue with Garmin Connect.