Ok, let's talk about the split duty case some more... You shouldn't have any alerts remaining after using the procedure outlined in documentation above. Typically, split duty trips CANNOT be imported with the importer and work properly (as of now). They will have to be manually entered to get rid of the errors. Make sure ALL flights within a single DUTY PERIOD (not "Day") are listed under the same duty period in APDL.
This would mean if you have a split duty trip that starts in the evening of Apr 1 (Wednesday) and ends the morning of Apr 2 (Thursday), in APDL you would need to create this as if it was only a 1 "day" trip. Flight 1 would be labeled with "WE" for Wednesday, the rest opportunity and flight 2 would still appear to be on the same "Day" of the trip (1 of 1) but the label will say "TH".
It should look like this and there won't be any issues.
If it looks like this, it's not done correctly and you'll see legality issues.
I'm adding these screenshots to the documentation to make it more clear.