I can't perform a re-installation of OS3.9 as i would lose 3gb of data on my hd!
Yes you can. AmigaOS doesn't purge your hard drive when you reinstall but do a backup to be safe (especially of your startup-sequence and user-startup files).
But you shouldn't need to reinstall. SYS:Classes is a directory. The files in it have been overwritten with older, incompatible versions. Copy the originals from the equivalent directory on the CD. I think the BoingBags updated them further, so run those installations to be on the safe side (there are ways to do it manually, but the installer is easier).