Maybe the Skrulls were crossing over from New Xander or New Mars, which seem to be the major alien-inhabited domains.
And if the explosion from Project 42 (which needs to have been in some sort of dimensional pocket rather than the Negative Zone, since the Negative Zone wouldn't have been around at this point) happens 6 years ago, then the process that took place from then on to create the division into Iron and Blue, including their equivalent of Secret Invasion and Dark Reign, clearly took at least some time, figure at least a few months before the division took hold.