Did the surviving peasants just go back to their traditional Chinese beliefs? Convert to other forms of Christianity? Keep their heads down so we don't know?
I've never been wholly pleased with my past answers on this topic, but here are the ones I'm least unenthused about:
The basic problem is that the primary sources seem lacking at best, and on top of that – and largely in consequence – the scholarship is just as thin. We have some information about the postwar fortunes of individual ex-Taipings, some of whom, like Hong Xiuquan's nephew Hong Quanfu, remained anti-Qing rebels long term. But information about their religion is pretty limited beyond awareness that, for instance, Hong Quanfu almost certainly died a Protestant, as he is buried in the Protestant cemetery in Happy Valley, Hong Kong.
Aside from a lack of material there's just a general air of uncertainty. There's no clear consensus on the religiosity of the Taiping subject population; the extent to which they saw themselves as Christians as opposed to part of a broader and more locally-rooted continuum of heterodox sectarians; the rough number of survivors; how many emigrated as opposed to stayed; et cetera. The above-linked answers say the same at greater length.