They will be regular seeds.
Having personally done exactly this, you end up with roughly one half regular photo period seeds, one quarter regular photo period fast/early flowering seeds and one quarter regular auto flowering seeds.
You will then have to grow many seedlings and cross breed the selected regular auto flowering plants to produce a more stable line of regular auto flowering seeds.
After this second cross with the regular male and female selected auto flowers to "fix" the auto flowering trait, you should get nearly 100% regular auto flowering seeds in the third generation of seeds.
If you want to breed the best line of seeds, you will have to/should grow 50-100 second generation seedlings and select the best two plants as the parent plants, as limiting yourself to just a couple of plants might result in very average offspring.
You really need to breed with the "best of the best".
Hope this helps, Organoman.