User blog comment:TVthePunisher/Final Getsuga Tensho and Isshin/@comment-2041622-20100916090050/@comment-1454424-20100916091140

That was most logical until this chapter. It's not like Kubo hasn't discarded everything that Isshin and Urahara said to each other during that conversation. The conversation implied that the Vizards willingly sought out hollow powers, Urahara was not personally involved with the Vizards, etc, etc. Besides which, the other explanation of that conversation is that Urahara might have helped Isshin regain his powers.

I think at this point, especially since Isshin was the one who told Ichigo about the Final Getsuga, the most logical explanation is that Isshin lost his power to Final Getsuga.