I guess using LHA on an A1200 to archive GB of data is not a good idea. For small archives <=10MB it is ok. For LHA options read the lha.guide. For DOpus output you can activate it where you define the LHA command line. Both LHA and DOpus have output options. CTRL + C should break LHA. In a shell you can type "status" to get the process number and with "break" you can break it. Scout/XOpa can break/kill tasks too.
If you are not fixed to fat32 for the CF card I would use the same filesystem that is used on the source device. Then use a backup tool like
http://aminet.net/package/disk/bakup/BackUp