Tobi used Kamui on the Amateratsu Flames
Much debates have come up on how Tobi escaped the “Black Flames” implanted in Sasuke to burn him up. Hopefully this will clear any speculation.
Tobi’s right eye
In this link, Obito is caught by Amateratsu while his mask is off, his right eye still has the sharigan
In this link we see Tobi unraveling his eye preparing to use Izanagi
Tobi uses Izanagi in this link
In this link we see that Obito has replaced the eye that lost his sight with the Rinnegan. Which make sense seeing how his sharigan would be useless.
TObito did not use Izanagi, he used Kamui. Whether he refilled or not is cannot be proven as it did not show that he used the technique nor did he talk of replacing his eye. Kishi simply displayed him off screen so that his abilities would not be revealed yet (in much greater detail).