I try to leave my modules in place as long as possible, because a) it's just no fun (even with knurlies) b) there's always a chance of plugging in something wrong (even with shrouded headers on the bus boards) and c) I hope I don't spread FUD but I've read somewhere that the Eurorack connectors are in fact spec'd for a number of re-connections that's in the double digits… [citation needed!] and I prefer not to test my luck too much. Still, I think I've rearranged >50% of my rack two or three times last year.
I have certain classic synth voice combos that I leave patched for a very long time. Also, I don't feel I need to mess with final fx->mixer->outputs wiring too often. In general I go blank slate when I feel like I'm completely stuck or actually done with a track. But that means I sometimes live with a patch for weeks and it gets very messy fast.
All that said, I do wish it was easier to rearrange everything. I agree, this thing does seem to have a life of its own. And the way modules are arranged has a huge influence on my patches. Most boring case, because I'm running out of long cables and mults…