Download a clean set of files for 1.2.5 to your PC in like /zen_new...FTP from your host the files for your current shop to like /zen_current.
Using a file comparator like beyond compare,(ZC's favorite) or winmerge perform a batch compare for all or by folder to define files that are different than the original core files. If they are not files that are in your override folders then it is these files that you should then on the host set, place in your override areas and replace the file in the core location with the clean copy.
This way you have in your override folders the edited files and then the upgrade will not cause you to loose these edits. Upgrading any time, One needs to then compare their edited files to those of the upgrade core files and merge these files so that your edited files contain any revised/new code from the new version.