For 1K-DFW's example...

It has always been United's 500 Miler policy to collect additional 500 Milers for any segments that clear after your first check-in that day.

You only get the first origin to final destination point-to-point calculation if all of your segments clear the waitlist prior to checking in for your first flight that day.

This has been the policy since long ago, even before E-Certs were invented.

If my ONT-DEN-IAH all clears before I first check in, it's a total of 3 500 Milers (for the ONT-IAH "point-to-point" total).

If my ONT-DEN clears before check-in but DEN-IAH does not, they deduct 2. Then if I later clear the DM list for DEN-IAH, they take an additional 2 for that, for a total of 4 (no longer qualifing for a ONT-IAH "point to point" total, but a simple but more expensive "per segment" calculation instead).