On BitD p158, it says
“Choose downtime maneuvres and advance clocks for the factions you’re interested in right now … Later, when you turn your attention to a faction you’ve ignored for a while, go ahead and give them several downtime phases and project clock ticks to “catch up” to current events.”
I interpret that as “Each time the PCs take downtime, each faction should advance all its clocks and take one or two downtime actions. But for factions you’re not interested in right now, feel free to do this only in retrospect, when you think it would be interesting for them to do something now.” (i.e. for any programmers in the audience, it’s suggesting you do lazy evaluation of faction development).
A less rigid interpretation is that GMs should advance some factions each downtime, and try to advance all of them sometimes, but not worry too much about making sure they get their “fair share”.
Former will give more consistent behaviour of factions; latter is more tractable, especially given a large active set (e.g. the BitD book has detailed writeups for 26 factions).
Do we know John’s intent here? How is everyone else doing this?