there is unnecessary confusion arising over this issue. Alain is talking very specifically about the backup from his hx6 hard drive from the techmanager program. These specific points do not arise for anyone without a backup performed by the techmanager program.
Since you have wisely backed up on floppy disk, you will have no problems, apart from the obvious one of re-naming the files from their 6 character floppy format to take advantage of the 16 character filenames available on the SD card. If by auto load (there was no auto load on the sx3 only the sx6) you mean fast load by number, this option is also available from the SD card.
The SD has a load by number feature exactly the same as your existing system, so you just need to replicate the folder/file numbers when copying floppies. The only difference was a maximum 16 files on the sx3 is now a possible 20 files per folder on the SD card.
Furthermore there are favourites scripts of shortcuts to any file and alpha sort lists which enhance the SD functionality beyond that you have been used to with the sx3.