Can the D4 put items back into the pool

the-binding-of-isaac-rebirth

I was doing a BASEMENT run and I got the D6, D20, and D4. Before breakfast, I used the D4 a few times and after a few more rolls (D6+D20 rolls), I got breakfast. I went to the next level and to my surprise, there were still items that weren't breakfast. I even picked up the small rock, which I distinctly remember picking up earlier in the run. Could the small rock have been put back into the item pool by the D4?