Again, no problem. I just add a migration script where I set "B.researched = false". But what if B is a prerequisite of yet another technology, C? If I've disabled B, the requirements for C aren't met and it shouldn't be available. So what's the best way to handle such cases?
I could ignore them, but this would look very strange, especially in upgrade chains (e.g. if "electric-energy-distribution-2" is available although "electric-energy-distribution-1" has been disabled). I could also traverse the complete technology tree and disable every tech with unresearched prerequisites. That would probably make me the most hated modder ever because I guess it would take some time until every technology has been checked -- and if my tech A should be an early technology (how about adding a prerequisite to automation-1?), running the migration could disable most of the already researched techs (think of a mega base where everything but infinite techs has been researched ages ago, until my mod was added).

(Apart from that: it's easy to go down the technology tree by looking for prerequisites of tech A, but there's no easy way to go up and find the mods that depend on A. I suppose there may be a reason for it …)
So, is there any recommended procedure?