We have this situation: there was an error in teh solution, which occured in one of JS files deployed into _layouts.
Bug was kind of a critical, and decision was made to push chaned JS file by hand into layouts folder (YESS, I know, not suppoeted etc. - will never do that again, promise!). And that worked. We also incorporated changes in IDE, not to loose changes for future release.
Along the way we made some other changes in solution, which also changed the JS file. We performed update of solution: uninstalling, removing, adding and installing again on web app. Everything worked, except our JS file, which was not updated and there is still a version of file which was modified by hand.
Did you ever had same situation? is it possible to overcome in some civilized way? Powershell maybe?