Sgt_Kickaxe - 9:12 am on Oct 26, 2013 (gmt 0)
There hasn't been a PR update in a long time so I'm not sure what change your referring to but to answer your question...
The internet is fluid, a change in one place can and does lead to changes in other places. Since Google places such heavy importance on links it is conceivable that you removing a link to a page with very low visibility, and with only a long tail keyword rank, might cause it to lose some positioning. That's highly unlikely however, there are many mechanisms in place that limit and delay positive change as well as many that dilute the impact any single site can have on the net.
Have you made sure you're not seeing personalized results for the sites you say are falling?