I haven't seen any research on the effects of silver on the digestive tract personally. Though I'm thinking the value of user experience and preventative measures may be sufficient in dealing with the potential risks that may come with drinking larger quantities of CS. ie, taking probiotics or flora building supplements etc.
That said in light of recent experiences on matters of sublingual CS intakes, I'd question the legitimacy of the impact of CS on flora in cases where the gut is bypassed altogether. And so from my perspective, the issue is easily mitigated with home-made solutions. Though perhaps not so easily with nano/microparticulate solutions(aka true Colloidal Silver ), as these may not readily diffuse under the tongue based on particle size /density.