"Id never entrust such important system files"
On AmigaOS the system files are the least important files of all. Standard setup is one system partition and one application partition. All important data goes to the application partition. For the system files you have the best backup you can find: the original floppy disks or CD.
The boot partition can easily be formatted and reinstalled without loosing any application data. There are only a few programs that depend on some files that install onto the system partition (e.g. ScanQuix, Wordworth). I've done this several times.
Of course you should not blindly format your boot partition now. Make a complete backup before.
lha -e -r -a a work:workbench sys:#?
does the job.
Bye,
Thomas