I was referring to re-installation of individual packages i.e. you install a package, find you don't really need it at this time and so remove it and then find later you do need it as opposed to removing ALL packages and then re-installing.
However, having said that, I have done this many times in the past and never run into any problems. It can take a bit of time if you have a large number of packages, but I've never found any need to take additional action with only 1 exception and that is with respect to org mode.
The only package which has ever given me any problems has been org mode and that was partly my fault (I was loading org functionality and then trying to install a later version from the org repo).
Of course, if your using unofficial elpa repositories, all bets are off as there is no curation of the content in these repositories. I have certainly found crappy packages in some of these repos. However, that is not something Emacs has control of and if as a user you decide to install packages from such repos, then you need to be willing to deal with the issues which arise.