All bacteria is wiped clean within about 10 days on a water-only-fast, but when refeeding begins, the beneficial bacteria are replaced in the biological process of digestion. I have never seen the need to consciously replace good bacteria at all and have had no digestive issues after fasting, whether of short or extended duration.
There is always that elusive evidence that people look for as in this case, but few if any scientific studies have been done to substantiate claims by the proponents of the fast.
Fasting supervisors over the last 160 years have also not seen the need to replenish good bacteria with supplements of the same, with no ill-effects, but only distinct benefit to the body. The laissez-faire approach (let-alone-plan) and allowing Nature having her own way, always produced the best results in the restoration of health and the eradication of disease.