All of the Es I've had that passed were in intact shells, while the ones I know to be wearing modified are still partying a year and half on.
It is a personal choice, but I've never personally seen anything that leads me to believe it's harmful. It's not like we're forcing them into an already modified shell, and they're going to do it anyways! What are we supposed to do, chase them out of their shells every few months and make them change into an intact one? It's what they want, and they're obviously adapted to it. If it gets them to move into a better fitting shell, then it's all the better. (Although they are adapted to wearing the tiniest little shells as well - those legs are build to be armor.) I pull shells when there are obvious holes through the outside, or when they get so thin they risk cracking, or so worn down that they are nothing better than a "cap" on their bums, but never for a missing center. (Course, I never get there in time either - all I find is the smallest modified ones since they've already had a changing party when one does decide to take the plunge and 'flip this shell'. 
)I can't say if the same adaptions hold true for other species. PPs may very well not be able to handle a modified shell. I've never had one come off a PP looking different, and since I have separate colonies they are never exposed to modified shells either.
I got video, but that's another story. I'll have to post it sometime because it is HILARIOUS.
Gotta love custom-fitted shells! 