According to Essentials of Oceanography (2012) at page 13
The physical expanse and distribution of the early ocean is a matter of some controversy. Most researchers hold that masses of rock have always protruded through the ocean surface to form continents. However, some recent studies suggest that water may have covered Earth's entire surface for some 200 million years before continents emerged.
The authors of A case for late-Archaean continental emergence from thermal evolution models and hypsometry Earth and Planetary Science Letters volume 275, pages 326-336 conducted 100,000 simulations to determine the fraction of the Earth covered with water 2.5 billion years ago.
The input parameters are described by Gaussian distributions using the mean values and standard deviations listed in Table 1. From [100,000] realisations, we predict a distribution of the area of emerged land and of sea level.
The Earth was completely flooded in 9322 of the trials
The medians for [area not flooded] range between 1.79 and 2.84% of the Earth's surface.
In conclusion, the research found a 9% chance that the Earth was completely covered by water, and the best estimate was the Earth was between 97.16 and 98.21% covered by water.