In looking at the GEDCOM report, it seems that certain profiles were deleted before import was complete. These were ones from before 1600, which was our cut-off. That is, we prohibited the auto-creation of profiles of people with birthdates before 1600.
That import was from before GEDMatches and all the import changes that went along with it. I think what caused this confusion has been replaced (with other things about imports that cause confusion).
Which is to say ... I realize this is a confusing presentation of information, and the are various things which could be clearer to the person who imports the GEDCOM and others who see the profile. But the import system in 2012 was completely different from what we have now. To talk about improvements, we need to be looking at a new import.