It looks like you have a couple things happening here.
First, APDL does not currently support "trip blending" which is what we call it when you try to import a modification to a trip on top of the part of a trip that has already been completed. That is why your import overwrote the entire trip. This is something we hope to introduce in the future, but for now, trips are imported whole...all or nothing. Additionally, if you import a different trip that overlaps an existing trip, the same thing will occur.
I'm not sure exactly what is causing your autofill times to come in incorrectly after the above trip overwriting issue. As you noted, the issue with the times being yellow is that APDL detects that they are out of order and it can't calculate a duration for you, so it prevents you from being able to save incorrect data.
One thing you could try, is to delete the actual times that you have, and retry autofill completely by using the "autofill now" button. Autofill will not overwrite anything you already have entered so this may help. If that doesn't work, you may have somehow gotten incorrect dates attached to some of the times in there somewhere. Check the DATE associated with all the times and usually that is the problem in these cases. Sometimes, Autofill will get confused if you have a significant delay and retrieve the times from a previous or subsequent flight that has the same flight number. If retrying autofill doesn't work for you, your last two options are to manually enter the times, and make sure the dates are correct, or wait until the trip is complete and reimport the whole trip from your company website with the actual times.
